Probably to bring the M3 in line with the updated ATC & ACSES implementation and to match the M3a on Harlem line
Doubtful. The signal system is actually outdated on the Harlem line. ACSES should work on the line like it does IRL, but doesn’t in game. Only the trains included in the route are compatible with the signals. - At least on the LIRR 2.0, you can use MBTA trains with its signal system.
I think you might be confusing Harlem & LIRR 1, ACSES definitely does work on the line and in both the M7a & M3a. But it seems the sounds were ported over but the nothing was changed in terms of safety system implementation. I also put the HSP46 on Harlem and the trains safety systems seem to work fine