The 18 or so miles from Wilmington Junction to Boston are roughly the same travel time no matter which route you travel if running express. Grade crossings don't really matter in terms of travel time, just less chance of a grade crossing incident. Double-tracking the Wildcat (about 3.5 miles) isn't without it's pitfalls on the Wilmington end, tying into an expanded, functional 2-track junction at the station may require a station reconfiguration and removal of a small building or two depending on how it's done.
But there really won't be capacity on the Lowell Line if/when service levels return post-COVID. The way Rail Vision was going there would be no capacity to route any meaningful number of trains onto the Lowell Line running high-frequency Anderson/Woburn locals. Downeaster is/was looking at service expansion, full Lowell service plus potential NH commuter rail (currently back on the table). The double-track from WJ to Reading (6 miles) is the easiest and cheapest option to re-install while building up capacity and requires only 2 station rebuilds, one being Reading which you would want to do under any local scenario anyway to make it a 2-track station.