Has anyone thought of the issues traveling around with the Harrier? It is an obvious Commerce Raider\Pirate. What keeps a system from impounding the ship once it lands? What keeps a Pirate Lord of Theeve from seizing it? The description will also be disseminated if the PCs are not destroying their targets. "There is not much cargo space in this, huh? Whoa, look at that particle barbette. Ideal for ship defense..." I understand about the attitude tracker by the system, but it still seems like this should be tough to deal with.
MTU, ships arent illegals. Crews can be wanted fro crimes. And if the crew is unknown the ship is marked for haboring a crew that is wanted for cimes. But if the ship and crew are clean, then there no issue.
I can see some highe LL system having issue with a somewhat heavily armed ship, (even though thats when they're least effective) and requring them stay out in orbit and have to take a shuttle to the planet side, and if they dont a shutttle and if you dont hav a sub ship, you're SOL, please leave.
As for why Theeve wont sieze it.
Sure, go for it.
Thats how most pirate ships are obstained, via theft.
Stealing the PC ship, has the issue that you can only really do it once, and then just isnt fun.
You also have to make it clear to the PC how ships are accessed when they're in a port, and what the crew SOP is when they are docked. And have them write out, abstract sop about what happen when the ship and crew lands.
This will help make it more fair and can also make it impossible for any outside force from taking the ship, without drawing too much attension from the starport, or damaging the ship.
Once it happen, the PC will probably try to make an SOP where the later will have to happen to take the ship.