I doubt this is about connecting/transit passengers, actually...I think these are more likely to be used to allow airlines more flexibility in which gates they use and which airline alliance they partner with without having to reconfigure or move their ticket counters. In the end, passengers will walk farther to get to their gates for their BOS-nonstop flights. It also helps to consolidate security checkpoints.
the C-E connector and the C-40s-B connector seem mostly designed to allow JetBlue to take over many gates without having to move from C, and to give Southwest E-C space so it can grow without moving from E.
In a similar way, I'm sure United is looking for a way to have one checkin that serves both its EWR/IAH/CLE flights and its ORD/IAD/etc flights.
If it were easy to move airlines (which it isn't) a grand swap that moved JetBlue to terminal A and Southwest to C or A2, and Delta or AA or UA to E (for "real" international connections) that would have worked better..