You're not wrong regarding the short gap in the discontinuous electrification plan being illogical, but I would point out that the
2022 Network Rail analysis of just the Providence/Stoughton Lines indicated that running on OCS would require an infill substation in Roxbury, let alone electrifying something the size of the proposed Widdet Circle yard. The same applies to the Northside; I actually think the NS sub would be at the CR shops where there's a better grid connection.
As far as the transit sub goes, it provides 600V DC to the 3rd rail/GL catenary, but everything in the distribution network until the TPSS is 13.8kV AC, every line in red on that map; I believe it's rectified down to 600V DC at the unit sub level. I would point out that some substations like those from Oak Grove to Wellington are clearly missing, but I believe those, like GLX, are directly utility fed with 23kV, stepped down to 13.8kV.
In essence, I'm not expecting them to power the NS Regional Rail sub off of the Transit side, I'm thinking the opposite. I'm expecting them to bring in something along the lines of a trio of 25kV lines for the RR side,
and add in the switchgear and a 25-13.8kV stepdown transformer. That's actually fairly limited as far as equipment goes - I imagine the NS basement is roomy enough that they have the slack space. and would enable the transit side to fail over to the RR side when one of the South Boston lines goes offline.