After implementing some more functions and some debugging, I am now able to boot from a virtual filesystem. All AmigaOS files are stored in a linux-native filesystem and mounted inside uae for AmigaOS to use:

It is still *slow*. I don't know if this is because of the missing jit, the many debug log messages or any other issues, but hey, it at least works so far :)!

Config file used contains:
filesystem2=rw,dh0:sys:m68k,0
uaehf0=dir,rw,dh0:sys:m68k,0
filesystem2=rw,dh1:work:m68k-work,0
uaehf1=dir,rw,dh1:work:m68k-work,0