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I thought about a particular example, and I was wondering if there's a problem when you use "where" in a situation where the thing in question are situated on the ship and not inside the ship. I don't think it's important, but I wasn't sure if it impacted the correctness of the sentence.
For example:
A spaceship where the guns are made of a titanium alloy.
This is idiomatic, at least in speech, but using something other than a place before "where" in this type of phrase is a little awkward and maybe not formally correct. I would prefer either:
A spaceship whose guns are made of a titanium alloy.
or (even better):
A spaceship with guns [made] of titanium alloy.
("made" is optional in the last one - omitting it gives a more dramatic tone, like "man of steel" or "heart of gold.")
