I don't really understand the structure of the different departments teaching computer science and engineering at UF, but it certainly sounds like a bit of a mess and over-due for a reorganization.
Even Georgia Tech, the first school with a College of Computing, still has a split with Computer Engineering still part of the College of Engineering but traditional Computer Science and everything else in the College of Computing. USF (Tampa) has both Computer Science and Computer Engineering in a single department within the College of Engineering, which seems to me to be about the most efficient structure. UCF (Orlando) had a Computer Science department in the College of Arts and Sciences and a Computer Engineering department in the College of Engineering but merged them together into one school a few years ago.
Even Georgia Tech, the first school with a College of Computing, still has a split with Computer Engineering still part of the College of Engineering but traditional Computer Science and everything else in the College of Computing. USF (Tampa) has both Computer Science and Computer Engineering in a single department within the College of Engineering, which seems to me to be about the most efficient structure. UCF (Orlando) had a Computer Science department in the College of Arts and Sciences and a Computer Engineering department in the College of Engineering but merged them together into one school a few years ago.