Not sure I understand the problem ...
First of all, Geeklog will not change anything on its own. It uses the paths you entered (in config.php, lib-common.php, and in the install script), whether they're right or not.
Then why do you think the install script is wrong? And what would be the problem with using the path it suggests?
bye, Dirk
P.S. geeklog.net is actually running on a FreeBSD server.