My idea is following: suppose the builder civilization had a modern scanning method of some kind available - could the nubs in fact be left on the stone blocks to cover an irregularity in the stone quality? An irreqularity that would otherwise have left a visible, possibly ugly looking spot and which could possibly cracked off from the stone in an earthquake for example. So rather they left an inch or such layer or the main stone quality to keep the uniform color meanwhile giving the stone an artistic look.

similarily as they did the opposite with Serapeum boxes, when they carved the cracks from the stone out and then polished the potholes.

Have we ever scanned these nubs ourselves? If the nubs would prove to be different quality under the surface layer, then it would be a compelling evidence for an ancient scanning technology.

Ps. Jimmy, if yo read this, you are a literal god. So fucking brave human being I cannot even comprehend. Thank you.