Is ”If I leave, it’s because Bob has arrived” ambiguous?
Yes, as it stands the sentence has the ambiguity you describe. There is no subjunctive here in either instance, but your (future) departure is contingent upon an arrival which may or may not have occurred yet.
But in actual use it has no such ambiguity. In real life, as opposed to the pages of a textbook, such sentences are uttered within a context shared by the speaker and hearer. You and your hearer will know whether the Bob you are speaking of is present or yet to come, and in that knowledge the ambiguity is resolved.