(I know nothing about this subject, feel free to ignore me.)
My dentist is pretty good at doing this too, by putting marking paper between my teeth and having me bite down. I wonder if a similar technique could be used:
Have the blocks close together, constrained to only move on a single axis by rails or whatever. Drape a thin sheet of material over one of the blocks, the non-moving one (perhaps it's an already-placed one?) Maybe it's something that visibly shows when it's crushed, or maybe it's coated with the blood of the powerless. Smash the other block into it. Pull them apart and look where they made contact. If it's mostly everywhere, done. If not, grind down or chip out the parts that touched. Repeat until you run out of innocents.
To do the very last block, you'd have to meld two sides, remove a block, fix up the other side, and then put it back in. Which might make this testable.
But I'm just pulling stuff out of my nether orifice.
If you only care about the two surfaces matching each other, you don't even have to worry about your indicator. Just grind them against each other, or use some lapping compound to speed up the process. If you want to get the surfaces truly flat, then you use three surfaces that you successively grind against each other.
https://www.ericweinhoffer.com/blog/the-whitworth-three-plat...
That's a fascinating link, and it sounds like what I'm talking about is what's called "engineer's blue" in the link.
But I think it would be vastly more difficult to grind two massive stone blocks against each other than to just ram one against the other. Not unless you stacked them, anyway, and if you stacked them I'm not sure if you could move the top one side to side in order to do the grinding. Maybe with some kind of grit, I don't know. Still seems harder.
Also, grinding methods end up removing more material (bad for teeth!), and I would expect more overall physical work to be done in order to remove that material (bad for massively heavy stone blocks).
As for making them flat, that seems unnecessary to me. But then, I'm not a pharaoh. (Even for a pharaoh, it seems like only the seems would need to be straight. Nobody could tell about the faces after assembly.)
Then again, after some quick researching, it seems like there's a good chance that the well-fitting blocks (which are not all of them) may have been cast out of a concrete-like slurry, not hewn.
https://www.shutterstock.com/search/millstone