What about giving the M3A1 some ability to actually scale into the late-game through the support role? It's not going to be on the front-line after the first 5 minutes and it's not that strong in counter-harassment, so give it something else.
I've experimented in the CE mod where you pay munitions to give it an ambulance healing aura so Soviets can choose to pay munitions rather than MP for healing, but there are plenty of other ways. Maybe some sort of stationary camo for scouting, mobile repairs, maybe have Kubel mini-map hack, etc, etc.
Your idea of late-game customization is quite good.
T3 unlocked Ambulance upgrade for M3A1, 50 ammunation then it can heal nearby infantry
T4 unlocked support-fire upgrade for M3A1, 50 ammunation and it can transport Mortar infantry to become mobile-Mortar or transport MG to become mobile MG car(lower-suppression)