As I see there is still issue with redeclaring function. I cannot check what exactly happens, but if you made appropriate changes in vBSEO file as described in installation manual, then the only idea at this moment I have is that some rule puts you back to vbenterprisetranslator_seo.php file - it shouldn't happens and I don't see how it is possible but without checking I have no other ideas right now.
Please go to vbenterprisetranslator_seo.php and made same edition as for includes/functions_vbseo_createurl.php - so find function vbseo_thread_seotitle and set the if clause around it. Please tell me does it help.
I understand your security issues - but still you can make forum copy - remove most content and leave only some dummy messages. What we need to help you is to go to exact configuration on exact server and see what happens and find out why. vBET is used by many forums - such things happens nowhere else, so unfortunately we are not able to give you answer from hand even if we would be very happy to help you.
About Define Homepage Aliases - we will made some experiments in this area. As I remember vBSEO freaks if redirect is made simply to "/", so we have to made internal redirect to index.php (it is not saw by browser) - defining your aliases would made redirection loop. We will check it again and see how to avoid this, but please remember that now you are talking about functionality of other mod and we are not responsible for its behavior - we give way to integrate with vBSEO, but still what happens inside of vBSEO it happens inside of vBSEO... Added in TODO list as to investigate this issue again. Also please try to define such aliases in htaccess under vBET rules - so it would give you 301 redirect avoiding leaks and vBET would be still able to work, since it would be before it not after (in vBSEO which would made 301 for vBET request). But please hold on with such experiments until we made vBET working fine on your forum.