I think the emulation will happen on WinUAE because even if Toni doesn't have interest in that bit, I'm sure someone else with those skills will. If there was OS4.1 classic emulation I would be more inclined to write things for it as I know my time investment is not gone when the machine fails. I always worry that when my (now 10 year old) hardware eventually goes all time investment in OS4.x goes out the window, so I tend to write for 68k because I know I will be able to keep using it in future.
I reckon it will be a good thing if OS4.1 was able to be emulated on WinUAE.