Hi Rémi,
I like the general idea personally. I use something similar on my setup, which is custom though, but I use the overlayfs itself rather than the FUSE variant (well since I could give it privileges, not suitable for distribution).
Is there a reason you're moving the registry files? As you said, they'll get quickly overwritten anyway and doesn't make much sense to me. Of course, to "solve" this you'd have to just set multiple prefixes in WINEPREFIX_OVERLAYS instead of their drive_c, and then the underlying mechanism will:
* Overlay drive_c. * Copy the registry (and dosdevices?) if it's not found on the new prefix, using same rules as an overlay would (i.e. the topmost one).
Well it might be more work but it seems more right to me. The FUSE layer will add some overhead, unfortunately. I don't know if it's significant for Wine/Windows stuff, but I'd imagine it can be if someone installs an application in drive_c somewhere in Program Files, which makes heavy use of file I/O.
It's a shame we can't use the native overlayfs due to privileges...
Obviously there's no point in trying to improve this further if it's not an idea worth pursuing for the Wine project. I just gave my 2 cents.