Again, this may be need by power-win32-users, who basically can't stand the GUI of "regedit". :-P
By definition, Windows power users are comfortable with the registry, as how else did they get to be power users in the first place?
PS maybe an alternative for the "winecfg" may be some cmd-line option like the "/advanced" to make such functionality available to user at run-time?
No, a totally undiscoverable "advanced" mode is worse than just regedit. Even an "advanced" button is bad: this sort of UI thinking is not one we wish to copy IMHO.
Sorry, but I don't see what your hangup over the registry is. Remember the .reg files are plain text! You can edit them in whatever editor you like (as long as no wine processes are running at the time, of course).