Not sure on PMT3, but I had a PMT2 in my E99 and it was supposed to have more clutch holding pressure than the PMT1. I dug around a lot before I did the swap and to me the PMT2 actually sounded better.
Not sure on the actual differences, but it seems they are mostly shift strategies. They are all the same family, and if you are chipped it doesn't matter because it's all being over ridden.