It is useful to remember that even when the DPP held the Presidency, they did not hold a hegemonic position in Taiwanese politics or state institutions or society as a whole. The transition from democracy was carefully negotiated so that the KMT retained influence over large swathes of the state, including the military and judiciary. Being in the Chen cabinet meant effectively working with a bureaucracy that was institutionally politically opposed to the Executive Yuan.
If the DPP wins in 2012, it is likely that a DPP President will face the same situation as Chen did, only worse, since for the previous four years officials and their contacts have been making hay with cross-strait deals and won't take kindly to seeing a shift in policy that constricts their profit margins or opportunities.