Maybe, maybe not. For m68k mac emulation it would probably come down to the performance of the PC version of Basilisk's m68k emulation versus UAE's since m68k Mac CPU emulation in Shapeshifter isn't an emulation at all, but more like virtualisation.
UAE's JIT has been pretty fine-tuned on x86.
Isn't Basilisk using the same JIT? just without custom chip emulation holding it back?