It's been too long since that name was in popular vernacular, as the name "Somerville Junction" didn't ever really have carryover coattails onto the neighborhood that grew up around the stop. It was always strictly a RR placemarker. The Somerville Jct. stop was discontinued in 1958 in the bloodbath of drastic B&M service cuts, the depot building being demolished sometime after 1947. Hasn't even been a major diverging point for train traffic since the Fitchburg Cutoff was severed in 1981, and the last freight train through the junction to the old MaxPak factory was in 2005. We're almost 3 generations removed from when it was last a wayfinding namecheck for anyone except northside commuter rail crews for whom it's still a named NH Mainline interlocking. Magoun is the nearest surface-transit point of interest, so it makes absolute sense even with it being 1200 ft. from ground-zero Magoun that it use that name for wayfinding.
Ball Square Station isn't in ground-zero Ball Sq. either, but we aren't going by B&M "North Somerville" (also lasting till '58) station naming nomenclature instead. That old placemarker is similarly meaningless to anyone who came of age in the last 60 years.
I'd argue that Ball Square station
is damn close to the epicenter of the commercial district.
I don't love "Magoun Square" for the GLX stop because it's
not in Magoun Square and it will never
feel like it's in Magoun Square. It's on the periphery of the residential neighborhood that is centered around Magoun Square. There's no opportunity for redevelopment to stretch Magoun Square towards the district, because it's surrounded by triple-deckers and housing developments. Yes, Magoun is the closest established
place to the station, but the square is far enough away that it's not a good way-finder.
The idea of where "the square" is won't move to be centered around the station. It will be where its always been and the station will be beyond the periphery. The area around the station is just housing. Lowell Street between Highland and Medford St is a currently a drag strip, though the city has doing a good job traffic-calming it. The station will much more be for residents going elsewhere and coming home than serving the square itself. Magoun square sits between the Lowell Street station and the Ball Square station, which as I said, is much more adjacent to the eponymous square than Lowell St station will be to Magoun.
IMO a station shouldn't be named after a square unless it a) opens up into the commercial square itself, or b) has redevelopment opportunities to connect it to the existing square.
That's why I'd rather the new station just be called "Lowell Street" (like "Green Street" on the Orange Line) or just be given a new name all together (a la Somerville Junction). I don't particularly care that Somerville Junction was at one time a commuter rail station, and to be honest, I came up with the name before I knew about the old station.