Ok. So I've solved the problem by approaching it from a completely different direction.
Instead of trying to move the characters to a new 'hardpoint' in the bridge set, I've simply created a new animation file for the seated locations of every modded bridge I want to include.
By copying the existing "GalaxySeated01.nif" animation file and offseting the body of the chatacter, I can match it up with the captains chair of any set I want.
Next, I added a new reference to this animation in the "commonanimations.py" file.
After that, I just change the character's .py file to represent the new animation ID under the "SetLocation()" function, and thats it!
Works for any character that I modify the files of. The hardest part was tweaking the offset values to actually get them sitting in the chairs properly, but it was just a matter of trial and error. The great thing is that the same procedure can be used to replace the crappy 'background bridges' that many of the alien races use as well. Makes the NPC dislodge much more immersive.
Thanks to everyone for the help, especially Lurok91!
Hopefully this can help others who want to do something similar in their installs.