Indeed, they have to work with what's available.
The "advanced" short-season leagues are the NYPL and the Northwest League. It would be difficult for the Phils (or any club) to have an "advanced rookie" team near their spring-training complex, since both these leagues are in the northern US, and spring training sites are not. Moreover, it makes sense that short-season leagues are in northern locales - that's a function of the weather. The Phils have done well in recent years, in moving their summer-A affiliate reasonably close to Philadelphia - where it's not onerous for the development staff to get to see them. Williamsport is three hours away - but that beats Batavia, NY (or Bend, Oregon, for us old-timers!).
They could theoretically move the High-A club to a closer city - the Wilmington Blue Rocks, in the Carolina League, would be the obvious target. But the Phils own the Clearwater franchise; they don't have a PDC with a separate ownership group, so moving the high-A club to the Carolina League wouldn't be a simple "end one PDC, initiate a new one" thing. They would presumably want to divest the Florida State League franchise, which would complicate their relationship with the city of Clearwater (some other club's high-A franchise in Spectrum Stadium, with the Phils' training complex literally next door?)