Hypothetical example:

You have a standard measuring stick of length 1u. The guy at the quarry cutting blocks cuts them to 1u (or 2u or some other small integer multiple of u) because that can be conveniently measured by stick. The guy making measuring wheels makes them 1u radius (or diameter or whatever) because, again, that's convenient to measure by stick. But the guy responsible for surveying the whole pyramid base uses the wheel because it's easier to go "100 wheel rotations that way" than mess about putting sticks end on end hundreds of times.

Several millennia pass and some conspiracy nut looks at the number of blocks per side and it comes out to a round number of multiples of pi. OMG, what were they trying to tell the aliens etc.

Yeah measuring in diameters is pretty strange but it was the first thing that poped into my head that would yield factors of pi.

Could also be that they a standard unit (1u) and would use both 1u radius wheels and 1u circumference wheels.

Or its all derived measures like "the length of a wheel spoke" and "the length of a string around the same wheel" so never the actually physical wheel is used for the measuring.

Maybe we should ask the tired archeologists?