I haven’t tried any of this, but here are some ideas:
You could try adding ‘NewShipType.formationSpacing=X’ to the ship file and see what happens. Use a really large value, like 5000, to see if it’s working.
Or maybe the position is still defined in mothership parade file? Try placing them over each other instead of next to each other in there maybe.
Maybe if you add a line for a carrier in the carrier parade file it will place it where you want. Maybe it’s placing them according to file we don’t have access to or in the misc slot, but if the carrier position is defined maybe that preset will be overridden?