From my experience doing the APs, it seems that hardly any of the ships are strictly legal. I think this is due to the fact that the original authors didn't build them to necessarily be legal. They are likely just focused on the story and aren't number crunchers and thus forget to ensure compliance (or don't care given the specific situation in the story).
I saw similar stuff when doing Pathfinder adventures. I don't know how many times I cringed when I saw an entry like "masterwork mithral chainmail". Psst, hey original author... there's no such thing as masterwork mithral. Mithral items are always masterwork to begin with. I must have corrected that one about a dozen times.
So I'm not surprised that the ship BPs would not necessarily be legal for most of the AP ships. It's just something that you have to take as normal and not let it bother you as a GM.
EDIT: I do appreciate deer_buster's comments about AP starship BPs. That's what I am attempting to build upon. It's a good thing to remember that the AP ship BPs will likely be out of compliance and therefore avoid bug reports on noncompliant ships that we literally cannot fix due to noncompliance coming from the source, rather than from the FG development of the ships.