I was pleasantly surprised you actually brought that one up. It's true that TI would always be in the back of Beijing's head, but I don't think they would regard it in the same light as Xinjiang separatism. Taiwanese are unlikely to become terrorists, or to have support of global Islamic radicals. FLGers don't seem to have much concerns in HK, although I agree that the PRC would be sorely tempted to put a lot more troops in TW than HK simply due to its strategic location.I think it would basically boil down to how much autonomy Taiwan would recieve, which in turn would depend on how good the negotiators on each side were to be. Political reform on the mainland is less of a factor IMHO, since hardcore TIers would not care how democratic the mainland is (the same is true of anyone, Taiwanese or mainlander, who would hold their political beliefs as dear as if they were religious beliefs). However, events on the mainland (and HK) may turn fence-sitters one way or the other. You're too young to remember this, but the Qiandaohu incident caused many Taiwanese to turn to TI.
Nonpeaceful reunification would be a lot uglier.