Yeah, if you were to all of A division stations to B division specifications, you would have to get rid of all the A division cars, because they would be far too narrow to be any use with the new stations. Modifying them is out of the question, unless you want to screw a sheet of plywood or metal onto the bottom of the doors to bridge the gap, a unsafe and ineffective option.
Shaving A division platforms back to be able to accommodate wider B division cars would not be practical. Some stations have narrow little island platforms already, and now whacking 10 ft off them would be just too much. Plus lots of tunnels would have to be widened to accommodate the wider cars (tracks would have to be shifted, switches realigned, support beams relocated, etc.)
Widening B division platforms to accommodate narrower A division cars could be done, but you would lose all of the capacity on the wider trains. Therefore lines would become dangerously over capacity. To avoid this, you would just need longer trains, but then you would have to lengthen platforms, buy more cars, etc. Plus you have these shiny new R143's, and R160's (and the future R179's by this point) that would be no use at all.
If it ain't broke, don't fix it. And the 2-division system now ain't broke.
Bottom line: A good idea, but not practical or cost-effective.