I have AF 2016, but the latest version of WinUAE has some enhancements for AmigaOS 4.1 such as the ability to use the UAEGFX drivers for higher resolutions, and (I think) mounting Windows drives. AF 2016 still uses the older version of WinUAE. So I just use the ROMs from AF and I have a standalone copy of WinUAE for OS 4.1.
There are some limitations (no desktop compositing, limited RAM), but it works surprisingly well overall. You can use the 68k emulation inside OS4, but then you're emulating a PPC which is emulating a 68K, so that's not ideal. I use AF 2016 for the classic 68k emulation.
