The directory change was "forced" by current versions of Windows: they don't allow a normal user to have write access to the program directory. So ADOM now handles this the same way other windows programs do, i.e. the program files and data are located in separate directories. Many commercial programs/games use this mechanism.
As for the "adom.prc" file, I'm very much aware of the problems caused by it. It's already been on my "TODO" list, but since the prerelease was kinda "rushed", there was no time to fix it before the release.
“It's a cruel and random world, but the ChAoS is all so beautiful.” ― Hiromu Arakawa