I was just wondering, would the navifate surface skill work for navigating the insides of a starship or space station?

It works within a Hive and given how large everything is in 40K, I don't see why not.

Navigate (Surface) covers the ability to navigate across terrestrial environments from frozen tundra to sweltering jungles, as well
as navigating man-made environments such as hive cities or subterranean complexes.

I.. it had not occurred to me, but I can't see any other Navigation skill applying.