BuddyPress.org

You should set your slugs in wp-config.php

Comments should be fine in bp-custom.php – there must some error in the way you have the file set up

Ps you are right that functions.php is theme specific, and bp-custom.php is install wide. However there are also order of invocation issues.. They don’t happen at the same place in the initialisation.

For slug and URL mods have a read of the documentation on here