It's a rip-the-bandaid-off shutdown, max pain for fewest total days of disruption and soonest benefit to the weekday schedule. If they tried to keep something operating this would take months, if not a year, longer to wrap.
Inside-128 is inoperable for any sort of truncated train shuttle because the signals will be totally offline inbound of Brandeis. Outside-128 they've been using these weekend shutdowns to do more work on new South Acton station, which has to get finished before the weekday schedules can increase. And that's why, in addition to meager ridership, there haven't been any calls for train shuttles. Don't forget as well...heavy construction also ongoing at Wachusett Station, and they can pack more disruptive work on the weekends if the freights have extra schedule padding Ayer-Fitchburg sans passenger traffic to pause longer around construction in Westminster.
That's the reason those places have been OK with the inconvenience. It's what's keeping their new station construction and peak-hour weekday schedule increases on-time for their debuts.
Inside-128 is well-covered by existing bus routes at Belmont (74), Waverley (73), and Waltham (70) that terminate at the Red Line inbound, and Brandeis U. is out-of-session for the summer. No shuttle buses necessary with those options. Outside-128 the ridership is too meager on weekends to justify the expense of running shuttles that far out of the bus district. The towns have been well aware for over a year they just have to suck it up, and haven't complained because the weekend shutdown dates for each construction segment have held firm so far. Ski season is the only time weekend service has any sort of measurable economic effect in places like Leominster and Fitchburg.