Well, in my opinion, part of the benefit of being a hospital employee is getting to dissociate yourself somewhat from the business aspect of the whole deal. A hospital-employed radonc isn't going to be as involved in making decisions about the allocation of capital as one in a freestanding center, so short/medium-term business decisions which would be based on the physician fee schedule would be off his/her plate. As a private practitioner in a freestanding facility, your income will be much more closely tied to the fee schedule numbers.
I could be wrong, of course: If your hospital contract depends on any of the numbers that come from the fee schedule, then you'll see a difference in your income based on those changes. However, when I was interviewing for private practice jobs with hospital systems, this was not the case.