By virtue of the fact that these bases might be used against China in a war. In the event of a conflict, China will not only bomb the places, but also reserve the right to go in there and use i as its own base. It will leave rest of Philippines alone, but as long as America has troop there, it gives China excuse to not only take the base (which they can do easily), but put a small operation there where it can make sure to jam any possible help that Philippines may provide to us military. I can blockade Philippines and give it a choice between economic blockade vs continued trading with China and having base there for the duration of the conflict.
Because Philippines is so much within PLA's attack range, the entire base seems like just such a dumb idea for us military
Occupying those bases seems exactly the kind of needless overreach America is hoping to provoke.
Those bases would be easy to take, but hard to hold tactically, especially in terms of logistics and defence, since the US and allies could easily supply the Philippines with long range rockets to spam at the bases from extended range.
Strategically, such a blatant land grab will not sit well with China’s other neighbours as well as with the global south.
The only PLA boots that should even remotely be on the ground there would be limited numbers of special forces for high value asset extraction/elimination missions, which will be short duration missions by its very nature. There might be scope for more marines to be deployed to secure the bases while combat engineers rig up enough HE to make it practically impossible to try to return them to operational worth for the duration of the conflict. But even that is far fetched, and would in my view be the extreme end of PLA counters for the bases.
As for punitive action against the Philippines should those bases be used against China, well Scarborough shoal will become a new mega base on their front door, and PLA missile strikes can erase their power generation capabilities and return them to the pre-electrical age. That should be punishment enough in the short term.