You are mistaken. The native chipset is still supported in OS4 on classics. Even hardware banging stuff tends to work since the hardware being banged is actually present.
Stuff that is critically dependent on 68K v custom chip timing might not work so well but then that's often a problem for faster 68K processors too.
Unless you are talking about using UAE on the classic machines, in which case, yeah, it's pretty slow.
Must say that some kind of "Radeon is emulating AGA, or FPGA on SAM 440/460" would be nice thing to see just because with AGA chipset not being emulated and Petunia 68k JIT it would make OS 4.1 backward compatible without need for UAE + almost all WB and productivity apps working.
In these terms Classic OS 4.0/4.1 is most backward compatible OS 4.x just because AGA is onboard (and supported by OS), making UAE mostly not needed.