I think in order to be consistent with the -r and -sd (Windows only) startup flags and environment variables on UNIX, it might be better to change userpath in finish.m. This way, if a startup path is specified, it does not get overwritten. I would simply add:
to finish.m. This way also handles the case where the last directory is deleted after quitting MATLAB.
Then in your startup - preferably not in the $matlabroot directory, then all users will get the same behaviour, and as GB Shaw said: "Dont do to others what you want them do to you - they might have different preferences":