It's very simple to deal with this situation. When it comes to ships and fighters Fleet Officers always have full authority, even with fighters. I don't think it's common for commandos or other troopers to fly fighters or any crafts in star wars. I understand there might be undercover assignments and stuff but if it's official whoever is sending SO would have contacted fleet and stuff. Plus it's not like fleet would intentionally stop SO if there is no reason to, so requesting ships and permissions would always be granted. As for Troops in the bridge, you did see troops working alongside with Fleet and Navy, however just like in the medbay if you're interfering or on the way and you do have clearance, Navy should be allowed to request you to vacate the area. As for unauthorised flights, there is a reason for authorisation of flight and ships, so shooting down an unauthorised craft shouldn't be out of the question if it doesn't comply to orders, just like it's done in real life. If an unauthorised craft is in your airspace, you're likely to shoot it down if it doesn't comply, the same can be said for unauthorised launch and stolen crafts. We shouldn't have to use excessive force between ourselves and we should respect one another.