Initially I found a line in "freelancer.ini" with an entry for a "story/static mission DLL" that got me thinking, so I tried commenting that line out. The result is you start a new game with the Starflier in the "FP7" zone (Omicron Major), which unfortunately doesn't have any exits.

So then I renamed the FP7 zone and copied the LI01 zone to be FP7. This results in you starting southeast of Manhattan with a scrunched navmap. Docking with Manhattan and exiting puts you back in the real LI01 zone, but there are absolutely no ships around and I couldn't use the jumpgates. Even commenting out the "locked gates" entries of 'initialworld.ini' didn't remove the access denied restrictions on the jump gate I tried. So it's a start, but I don't know what script is the "first" one (to keep the story DLL but remove the story scripts and keep the ship), or where the starting position is determined.

Next shot was putting the "story DLL" back and removing the script action from the M01A INI file responsible for the bar. This removed the "bartender greeting" sequence, but left me without a ship. I would've tried to de-rail the mission sequence after accepting the ship but I couldn't find it tonight.

The "newcharacter.ini" file doesn't contain the single-player start location...but perhaps someone else can find that, or the first script.