The real mystery is that we have no hint of how those feats were achieved, or achievable, with technology they plausibly had access to at the time. There is no hint of remains of tooling that could have been used to produce many of the artifacts. Modern stonemasons have nothing that could do some of it, e.g. the Saqqara boxes. There are no aliens to invoke.
People did things that we have no clue how they did, or even of how they could have done them. What is offered -- copper chisels -- is just wildly inadequate.
It is not surprising that historians and archaeologists are not, as a rule, up on that material. But they have no excuse after it was explained to them.
There is also the question of how the boxes were maneuvered down those tiny tunnels that would not admit enough people to do the work.
The Egyptian state outright collapsed at least thrice, and was successfully invaded at least that many times. I find it easy to believe that during one of those collapses, some knowledge about construction was lost.