I also did a test running a Classic WB HDD image configured with FS-UAE on the PC and running it with RetroArch P-UAE, and it runs pretty nicely as long as the system specs are kept modest (MC68020EC). The image is loaded with WHDLoad games which are fairly easy to launch through using the controller as a mouse, so no need to configure every game manually on the Retroarch side.
Like you mentioned, P96 will not work, but the normal screen modes including hires overscan work without fuss. Also saving back to HDD image is no go and every change made with settings, installing new software etc gets wiped out with a reset, which makes it a bit harder to tweak the image to my liking.