Don't even bother trying to figure out US military naming schemes.
I suspect that the reason the A-12 and the B-2 looked alike is that there is enough similarity in mission that the best shape ended up that way. (Or as an old friend used to say, "aerodynamics can't lie.")
Knowing the CIA, that designation may have been misdirection too. 'Main battle tanks' are called 'tanks' today because of WWI era misdirection. Instead of calling them "armoured tractors" or something descriptive like that, the British called them "water carriers." The abbreviation of that (w.c.) was considered crude though, so they were renamed "tanks" as in a container for carrying water. This was to ensure any German spy who overheard the wrong conversation would get the wrong impression.
The Lockheed A-12 has a familiar appearance... I always thought it somehow looks like a flying dragrace car. Everything in it screams "fast".
And as for the "wrong" (McDonnell-Douglas) A-12, another thing I found interesting was that some of the modern drone designs also have the same triangular shape. (Like X47-B, X45-C/Phantom Ray, nEUROn, RQ-170)
And the X47-B can even fold its wings!