Secret Runway outside Edwards AFB

The first thing to keep in mind is they don't fly anything secret during the day unless it can hide in plain sight. A uniquely shaped plane wouldn't fly during the day. A conventional plane with modifications could be flown during the day. [Think of all the documented Groom Lake daytime flights. They have all been known airframes. This is probably more true for the Tonopah Test Test.]

I've hiked the area around the Tejon RCS many times. It is buzzed all the time by light aircraft. They have a few Long EZ owners out there.
Long EZ

Long EZ

Long EZ's are the biggest source of daytime UFO or UAV sightings. In fact, some USAF bases keep a LongEZ on hand to act like a UAV for training.

The amusing thing about this is that the Russians and Chinese probably know more about this project than US taxpayers.

During WW2 an ALSOS team in France found the Nazis had transcripts of phone calls between Roosevelt and General Groves about the Manhatten project.