By 'perceived problem', you mean, 'massive fundamental flaw', I assume? Hmmmm.
This has nothing to do with disliking fps gameplay, btw. I played about a thousand hours of Overwatch. So stop coming up with ridiculous reasons why I must be some sort of anti-fps prude. In fact, I think it could be quite good, IF it's done in a reasonable and efficient manner. On board ships simply fails to qualify for either of those metrics.
It takes more than just fun. It must be fun AND rewarding, or people will do it rarely if ever. CQC is very fun, for example, but also very rarely used. I personally only do it when I have 7 friends to do it with, and that only happens very rarely.
And besides that, there's zero reason why boarding a ship is a requirement for fun. The exact same player activity is going to be happening on the ground - fps combat - so who cares where it takes place? Except of course, doing it on board active ships causes a huge number of potential problems that a ground based arena does not, and requires an exponential increase in dev time, most of which would never even be relevant. Who's going to board an adder or a sidewinder? 90% of the ships in the game would have content that would never see use.
On the opposite end of the spectrum, stealing ships is just never, ever going to happen. It raises a huge number of problems. Can you just steal engineered modules? If not, why not? If so, you've just created a way to duplicate engineered stuff, which is insane and never going to happen. And even if it's only 5% of the total sell cost, many ships are worth over a billion credits. You're talking about giving players an exponential leap in income for 10 minutes of fps combat. Who cares about cargo piracy at that point, the money's in selling the ships.
The biggest reason why NOT to do ship interiors, especially in regards to fps combat, is because you don't have to. FPS combat works far better, and with far less issues to address, in new, purpose-built areas for this to take place. Trying to force it to work on ship interiors is forcing a square peg into a round hole. Even if you could potentially get it to work, it'll be ugly and not very practical.