The Inland Route has been a topic of discussion between MassDOT and CSX ever since the mega line buy /ops relocation deal of 9 years ago. That wasn't a one-time asset transaction and grant for upgrades; things have continuously been happening for a full decade directly and indirectly related to that deal. Some are brand-new funding items now grinding into gear like the Framingham Secondary and Cape Rail upgrades meant to strengthen CSX's business from Mass Coastal interchange. And others are informal like a continuous dialogue over the NNEIRI/Inland study. That study did not get cued up without CSX's tacit approval.
Have to remember: this is NOT the bad old days of "We're Conrail; our whole existence is about prepping ourselves for megamerger/buyout, so screw you little gnats." And CSX is not some irrational ogre like Pan Am. When states tickle their profit centers in negotiation, like MA and MD have to great productivity in recent years, they are wholly rational actors who cooperate enthusiastically. Yes, they do drive a hard bargain as any conglomerate would, but they will talk to anyone who speaks their business language. On the flipside, when negotiations are hostile or passive-aggressive...like in NY State over Empire upgrades on the Water Level Route...they are quick to remind "we crap bigger'n you" and then show it in their actions. The difference between the states they mesh with and the states they don't is that the states they don't get along with often refuse at some basic level to talk a business language. NYS wants all kinds of enhanced passenger rights and ability to do passenger-centric upgrades to the Water Level Route...but they won't say anything about pushing some money around for transformative yard upgrades or helping CSX troubleshoot why its east-west lane lags behind its overstuffed north-south lane in direct competitiveness with with NS. When Albany pols start acting out like they're insulted that a for-profit company would dare want concessions that maximize its profits, of course it's going to get chippy.
Not every situation automatically leads to the worst-case "Ooooh....better watch out! CSX are bastards!" doom-and-gloom. The last 9 years of them in this state couldn't be a bigger counterpoint to that. So beware of the overly pessimistic prevailing assumption based on bad-old-days Conrail. If the Inlands are being negotiated on a continuum outflowing from the set of much bigger deals hatched a decade ago, then something has to overtly change with the manner of that public-private discourse for new fault lines to suddenly start appearing where they didn't before. That doesn't mean there won't be tough sticking points or potential snags. It just means that somebody's attitude has to pull a 180 for things that weren't deal-breakers before to suddenly become default-assumed deal-breakers now regardless of evidence or momentum. The Inlands aren't a negotiation in a vacuum where every new discussion is alien to the last one; it's been a neverending conversation.
The costs for the upgrades that give CSX's intermodal profit center all the slots and ops flexibility they'd ever need are already baked into the base costs of the study's Recommended Alternative: contiguous double-track and certain number of new interlocking installations for overtakes at crossovers, uniform Class 4 track so CSX gains +20 MPH running speed on the Springfield-Palmer straightaway, minor curve easening in the Worcester Hills in tandem with the Class 4 uprate to take the sting out of some of the worst speed bottlenecks, and state-of-repair rollback (e.g. a lot of the same rail distressing that eliminated the summer heat speedos Worcester-Framingham). Those are all known-knowns. You're not going to see any kooky things like arbitrary track-by-track traffic separation get thrown into the mix this late in the game, because the Rec. Alternative they did present up folds in 10 years of discussion about CSX's base requirements for playing ball.
And we can assume that whether Amtrak is going to going to have expanded trackage rights under CSX or CSX outright sells the B&A under their feet and flips itself to trackage rights under MassDOT that there'll be the usual indemnifications baked into the agreement protecting CSX's alpha-status as the incumbent operator. All very similar to how rights/responsibilities with PAS were divvied up when the Conn River Line was sold, and in lesser degree templated when CSX sold off the Framingham Secondary. Things like: all the necessary paper barriers protecting CSX from competitive intrusion, guaranteed slotting and right-of-first-refusual retention of dispatch control (and where handoffs may or may not be adjusted around Springfield Union and Worcester Union), division of labor for track maintenance (MassDOT obviously becoming lion's share payee) + fee schedules for what share of freight-specific wear-and-tear CSX puts on the infrastructure + agreements for who the primary contractor is for doing repairs to what structures. For example, on the Conn River PAS: retains dispatch control, its MOW crews remain the incumbent contractor for any track work (on behalf of MassDOT or for themselves), and they have clear-cut boundaries for when they need to pay-in for maint or capacity management for their traffic demands vs. MassDOT doing it for the passenger traffic (e.g. there's brand new dropped CWR and tie piles for upcoming passing siding installations strictly to serve the expanding EDPL freight schedule). If you pull up the Conn River and Framingham Secondary STB filings you'll see every detail like that enumerated very clean-and-neat, with little potential for future disputes over chintzy things. CSX baked in a lot of the same clauses (admittedly with waaaaay more moving parts) in the set of '08 deals, and with its lease-to-own agreement with Amtrak for full ops control of Poughkeepsie-Schenectady on the Empire Corridor. The indemnification clauses in those filings are very much standardized, and not some kind of tortured, murky legal sausage-making. Both sides have well-acquainted with what freight profit centers need to be prioritized ever since Beacon Park negotiations started getting serious in the mid-00's, and have lots of prior practice putting those indemnifications to paper. Closing loopholes on future disputes is the last thing to worry about with how ho-hum these recent agreements have gone. The yearly NNEPRA vs. Pan Am flare-ups on who isn't doing what they're required to on the Downeaster corridor are very much the exception rather than the rule on how those things usually go.
What's not known yet is whether buyout of the B&A to MassDOT ownership is going to be the terms of engagement for moving forward on all this ^^^other mostly cut-and-dried^^^ stuff. Or whether CSX ups the ante and makes MassDOT have to take ownership of everything to the state line to zero out all of CSX's non-yard property taxes in the state. That all depends on whether E. Hunter Harrison sees some stock price-related haste for making a fire sale to trackage rights. But counterintuitively, EHH's pump-and-dump scheme may actually make the property price tag a little cheaper for MassDOT because CSX Corporate could see haste in making the best deal they can SOON rather than sitting on it patiently for years extra looking for an overpay. Keep in mind, though, that because of all those cookie-cutter freight indemnifications described above once they come to broad agreement on price range the transaction itself is not going to be all that complicated to pull off or be used as a wedge to take more hostages. They've already made several of those deals cleanly before, including over Worcester-Framingham.
And obviously there'll be some "Pimp My Yard" quid pro quo exchanged. But those pieces are also pretty cut-and-dried: MassHighway truck access & clearance improvements to West Springfield, and more investment in capacity/business at their shortline interchanges (NECR, Mass Central, & Pioneer Valley this time around). Maybe lathering on some other miscellany like offloading more territory on Mass Coastal while everyone's in the mood to make a deal...but the high-ROI items are all pretty well understood because they've been talking about them for over a decade and CSX wants to see some action on closing out these remainders before Norfolk Southern opens its double-stack lane on the Patriot Corridor.
But there's only so few things they'd be willing to fight over, much less walk away from negotiations over. They've already gotten 90% of their dream New England intermodal lane and ability to pare ops costs gifted to them from the state from all the previous deals. Follow-through on the final 10% of closeout items that have any tangible value to their profit center just isn't enough to wage war over. It matters that they get another follow-through push on streamlining IM ops and growing the interchanges before NS becomes a bigger player in New England, and the new cowboy in charge at Corporate may be in a much bigger hurry than the previous regime at dumping property for dumping property's sake. So while you could very well have some friction over CP 45 dispatch hand-offs at Worcester Union for the extra traffic or other such tough individualized nuts that need compromise or concessions...it's nothing that'll blow up the whole works. CSX has one eye peeled on what plans NS has for New England once they pay Pan Am to go away on the Pat Corridor, and CSX needs to fortify its own flank by getting these remainders flushed into action before NS gets the chance to start making its big push. They're well-incentivized to work for a deal, and not let a deal fall apart over something small and/or stupid.