Isn't this running an emulator in an emulator (x86 > ppc > 68k)? Or have I got the wrong end of the stick? If this was WinUAE just emulating 68k Amiga then I'd increase the sound buffers (with the side affect of increased audio lag). If there are no such controls then I think a faster PC is on order.
Yeah, the 68k emulation in WinUAE is disabled when you run OS4. You're trying to make an emulated PPC, which isn't 100% accurate to begin with, run a 68k emulation. It's essentially an emulator within an emulator - inceptionulator.
Other than for testing, there's no reason to use the 68k emulation in OS4 when you're running OS4 itself under emulation. It's a much better idea to set up a separate 68k environment with WHDLoad or just using the .adf images.
WinUAE itself runs great on my $100 Intel Atom tablet, both under PPC and 68k, as long as I keep the environments separate.