My DS7 is in a school-within-a-school program for HG kids. We transferred there mid-year, and I could not be happier. I think most of the GT programs in MN use the school-within-a-school model, which I believe gives the schools more flexibility. For example, unlike a charter school, they can set minimum test scores for entering kids.
Since I also had experience with a traditional school, I cannot see that there are any extreme differences in the school-within-a-school model, with the exception of the ability to group kids better by ability. The principal who runs the whole school is also in charge of the school-within-a-school, and the kids do specials with the same teachers as the other kids (gym, music). Our kids also go on some different field trips than the school as a whole.
The biggest difference for me was that my child is now with intellectual peers, learning at his level, and I don't have to advocate for more challenging materials all the time. There are still differences within a FT GT program, but the kids are grouped with peers, and the range of differences is nowhere near that of a regular classroom.
If you can, try to call some parents of kids already in the program. You can learn about the administration and other differences.