They wouldn't connect. See the link in this post for the proposed relocation plan. It's a 2-mile spur running along Route 28 dead-ending at the Bourne landfill. It's 5 miles away from Joint Base, and 8 miles by road from Cassova transload. It's completely, utterly useless and completely, utterly non-serious.This is from a March 16 article, but I'm not sure how new tracks constructed on the base would connect to the existing line.
"State Rep. David Vieira, R-Falmouth, meanwhile, said the Legislature is already considering a new rail-spur option for Otis Air Base on Joint Base Cape Cod that would, if necessary, replace the Cataumet tracks."
It seems to me that the possibility of receiving $20,000,000 in Covid stimulus funds is part of the incentive for moving ahead with the rail-to-trail option for Phase 4 sooner rather than later, but without a replacement for the existing spur I don't see how that could happen.
Bourne officials endorse Bourne Rail Trail plan, federal funds sought (capecodtimes.com)
"Sooner rather than later" is not going to happen, because MassDOT gets handed an instant loss in front of the STB if they try to break their trackage rights contract with Mass Coastal before the contract term ends. The only opening they have is during the contract renewal process, when they can aim to get the Falmouth Secondary excluded from any renewal. That's still going to prompt a legal challenge they may not win, but it's the state's best shot if they're going to side with the bike lobby. But it's almost certainly not timeline-compatible with COVID funds before they run out.