The vanilla game setup is as follows. The exit node of the pre-Leviathan cutscene on the Hawk starts the Prison Block module with a waypoint in the torture room as the custom destination. When loading that module, the player is inside a trigger, which has the escape setup script as its OnEnter. This script spawns a force cage on top of the player, then gives the player a safety jump back to the waypoint in case they got displaced by the cage it seems. The end of that script starts the cutscene of the three troopers discussing the chosen jail breaker. Later on, when the jail breaker opens the doors and control is switched back to the player character, the PC is spawned at the destination waypoint near the door, where they were supposed to run to from their cage (like Bastila and Carth do). During the development of the mod, I moved the PC's starting point back inside their force cage and quickly discovered a collision problem. It seems that placeables that are spawned via script do not rotate the PWK to match the rotation of the parent placeable. Which is a pretty big problem if the PWK is non-symmetrical. It appears that Bioware, rather than fixing the underlying issue, just didn't bother putting the player back in their cage. After a lot of messing about, I ended up adding the player's cage to the GIT, so the initial setup script was changed to remove the (now unnecessary) spawning of the cage. I didn't encounter any errors with the player not starting the module correctly, so I'm not exactly sure what the vanilla setup was in aid of. Maybe it was some issue on the Xbox that forced that approach, or maybe it was a legacy of the original boarding sequence scene that was cut. Although either way I still see no reason to have spawned the cage via script.
The vanilla script cannot be decompiled by DeNCS, but you can have a look at k_plev_escsetup_ATTEMPTED_RECONSTRUCTION.nss in the SOURCE folder for my interpretation of it based on the bytecode.
What I probably should have done is just nixed the trigger setup altogether and moved everything into the module OnEnter. But by the time I actually figured out what the hell was going on under the hood with the spawned placeable I had been working on the mod for 3 or 4 weeks and was kind of sick of the whole thing and just wanted to get it out the door. Plus more radical changes would potentially raise additional potential compatibility issues. At some nebulous point in the future I may add my own boarding sequence, at which point I would definitely rework the entire initial setup.
And yes, if you are using anything from K1R then it's likely got a whole bunch of incompatibilities.