the commuter agencies have to look beyond their own bumping blocks to determine what has to be or what can be done
Why must they "have to"? Because they might be forced to do so by Washington DC when no such thing ought to be necessary due to the pre-existence of an operator with all of the rights already in place?
Bottom line is, giving Amtrak the funds to become the operator of such rail services would be cheaper, and faster to implement, in both short and long runs.
I am just saying that it may take a new "tier" agency, between Amtrak and commuter entities (and perhaps created by Amtrak and commuter entities) to address the emerging market. These are the entities with the insurance coverage to whom freight railroads will talk
It's not solely a matter of "insurance coverage". Remember, the vast majority of large commuter rail agencies own their own tracks. It's also a matter of things like territory, running rights, route qualifications, crew hours of service and expenses, servicing facilities, terms of union contracts, et al. Commuter agencies are far less flexible than Amtrak towards startup of such operations, especially being state-based versus federal-based, among other things—and their equipment is not designed for comfort over several hundred miles of travel.
This would have been somewhat easier to do when Conrail was still in the passenger business, who themselves were "competing" with Amtrak in a sense (remember their "Crusader" between Reading Terminal in Philly and Penn Station in Newark NJ, for example, ostensibly under the SEPTA umbrella). But that era is long past, now.