Okay, my results so far are as follows.
No matter what save I use and where I place the code, STAG Units will not spawn at the Daedalus. No vehicles, no NPCs.. nothing.
Engine areas are not deadly, no change there.
Thermopylae: No vehicle spawns (except the Vtols that attack you at 5 star wanted level), NPCs do infact spawn, but only once the player sets foot on the carrier, and then they spawn in mid air and drop down.
I have read through mission luas, pasted about 2 pages of code around, but no luck. I seem to be stuck at that point.
Different thought, I tried preventing the mission M23, which is the Daedalus mission, to delete the groups and disable the Daedalus, but somehow it didnt work. I wounder if it is possible, to not edit the sr3_city.lua, but the missions directly do make the changes. Someone up for that? Ill keep trying nontheless, but as I said, I seem to be at a dead end.