It was a heavily classified project, as evidenced by the enclosure to hide its shape. I don't think they would want to be flying it out of Burbank in plain view of everyone. Additionally, its first test flight occurred at Area 51, after this move, which is an ideal location for testing such things. Test flights near a city are probably not a good idea.

All they have to do is issue a press release saying that it most definitely was not a UFO and the rest will take care of itself.

Had this been a few years later, they could've transported it via helicopter:

http://en.wikipedia.org/wiki/Mil_Mi-12

Perhaps, but then this Russian helicopter, which the US didn't learn about until much much later, would have taken it home to Mother Russia :-)

I also doubt they would have long enough runways in Burbank to take off with that beast.

Burbank is actually somewhat infamous for having one of the shortest runways in the US used by full sized jets.

It was being moved to Nevada for test flights. They had a pretty good idea, but no evidence at that point, that it would even fly. Later "production" models were flown to the test site.

Or alternately, to have built them in Area 51.

A great part of the success of Skunk Works, or at least what I took it to be from Rich's book, was how coupled manufacture and design was done in the division. About a cardboard wall as separation, with design ideas and manufacturing troubleshooting going back and forth.

So that would've been counterproductive.