Isn't the central artery alignment the only one that has protected right-of-ways for portals for all commuter rail lines? Don't you sacrifice some network connectivity (which is what NSRL is really all about, valuable network connections we cannot anticipate before deployment) in the other alignments?
My understanding is that under the 2018 Baker Feasibility Assessment, whether Fairmount and Old Colony get NSRL portals mainly depends on 2-track vs 4-track, not the alignment (Central Artery, State-Congress, Pearl-Congress). They excluded the South Bay portal from the 2-track alternatives likely due to capacity constraints in the tunnel.
However, in reality and in a less sandbagged proposal, not granting NSRL access to Fairmount is just ridiculous. Once you build a portal for Fairmount, that easily functions as a portal for Old Colony. And both State-Congress and Pearl-Congress alternatives seem to allow a South Bay portal to be added easily if you want to.
So no, a well-done design doesn't need to sacrifice network community as long as the NSRL tunnel still runs from South Station to North Station, regardless of alignment.