Well no one is doubting that the federal portion of the framework would be mainland-dominated, just like Germany has way more seats in the EU parliament than Luxembourg. But Taiwanese democracy (and military control) would be unaffected.
1. There is no scenario in which the PRC would relinquish military control
2. Germany makes up 18% of the EU’s population. The PRC makes up 98% of the combined populations of Taiwan, PRC, HK and Macau. That is quite the difference in lopsided power balance.
The PRC wouldn't have to relinquish military control, or really any control for that matter. The "Union" is basically the portion of control that Taiwan has already ceded to China. The key is that Taiwan retains the rest for the time being.
