Would it actually be a game over if the nautiloid crashes though? Best case scenario the game dumps you in a different location and you get a slightly different start.
Well... if you run out of time and the nautiloid crashes, it would be in Avernus. I somehow doubt your character(s) would have a fun time there, considering the blood war and everything...
I think there are likely two options:
1. You die, and have another crack at it starting from the initial autosave when you entered the helm
2. They have some ridiculous animation that gets the transponder connected regardless
My money's on option 1, because option 2 is objectively a horrible way to start the game
