The script I used manually overrides the WinUAE configuration paths using WinUAE command line options in a .bat file (which I converted to .exe as the launcher).
I installed it to My Documents, installing to Program Files would require administrator access when running to change the AMOS config files, etc.
(Merge post) Apologies for thread hijack: I removed all absolute paths, this build seems to work correctly now using its launcher (.bat or .exe) in mounting the HDD directory from anywhere.
This installer seems to work on Wine / Linux too (subject to the usual Wine/WinUAE "F12" bugs).
P.S. Excellent work Toni!