Oh, yes, in those cases it'd be extremely terrible.
With DID/MPD, I think most people would just have to deal; there'd likely be GID either way, unless the other personality decided to deal. Majority rules, I suppose, although I suppose it could be a risky thing either way.
I've actually heard people trying to chalk GID up as BDD. Which just doesn't work...
As for the last one, I haven't heard of that one before. That's terrible. While I do think a person could be legitimately trans in conjunction with that, you're right that it'd be terrible to prescribe HRT before looking into any other problems.
Knowledge is power.