I don't think that it is obvious to most of the other characters that it is a patronus that is hiding Bellatrix. It would also be discounted because she remains invisible under the cloak after Harry's patronus is extinguished in Ch. 56.
Canon Dumbledore would have observed the masking power of Harry's patronus, and would be clever enough to to guess that the Harry's cloak could have this property. Presumably the HPMOR Dumbledore is at least this clever.
Dumbledore however observed Harry's extreme response to an unshielded dementor, so he might be confused at a Harry that walks around unprotected and apparently unaffected.
Working against Harry is that Dumbledore's patronus could be used to identify Harry's patronus as the one it observed in Azkaban, and that any dementor that observes Harry, and survives, could also identify him. It seems that if Dumbledore wants to later verify or exclude Harry as the intruder, he can.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.