Question:
I am curious though, why the LVT and APC counters make units combat/motorized, but the transport counters do not. This does seem to create a problem for the Americans in 1943, since they cannot form large stacks of full AEC/ATEC units.

Answer:
Transport counters represent trucks, with which the units are not used to co-operating regularly and mostly serve to get the units to the battlefield; think of a transport counter as a bus. APCs and LVT represent armored vehicles — “defrocked Priests”, Kangaroos, and the like for APCs, and Buffaloes for the LVTs. Units were meant to operate on the battlefield closely with these vehicles, hence the AEC/ATEC effects. And considering the number of c/m sub-divisional units and armored divisions running around, I have never found any of my opponents not being able to form large c/m stacks with the Allies…

Source:
TEM 53