Thanks for bringing all these points up! The additional ways to enter the Sith Military base are certainly interesting and could be worth a look at if it could be made to make sense within the story.
After you pointed out the issue in the Undercity, I did some looking and it appears the script that gave move instructions to party members only accounted for two party members as a third member isn't supposed to be with you yet. The third party member would tag along a little ways and would sometimes pass the trigger that would close the Undercity gate, but rarely. I have changed the script to issue instructions to a third party member and the infinite cutscene issue seems to be resolved. Thank you for pointing this out! I will make sure you are credited as I would not have known about this otherwise.
IMPORTANT PLEASE READ: IN V1.0, HAVING T3 IN YOUR PARTY WHEN TRYING TO SAVE HENDAR FROM THE RAKGHOUL CHASING HIM CAUSES THE CUTSCENE TO NEVER END. IF YOU ARE HAVING THIS ISSUE PLEASE DOWNLOAD AND INSTALL THE MOD AGAIN AS V1.1 & BEYOND ADDRESSES THIS. IF YOU DO NOT WISH TO REINSTALL THE MOD THEN DO THE FOLLOWING:
1) You can do this portion with only one other party member. It's only when T3 is present with a second party member other than the main character where the issue seems to arise.
2) Open the cheat console and type 'warp' without the 's and hit enter. This will force you out of the cutscene. Walk forward a little until the door shuts and then you can fight the Rakghoul as normal.
3) You can leave weak Hendar to his fate and bypass the issue altogether.
Thank you to N-DReW25 for pointing this out!