You do come up with some fantastic questions!
I'm not on the ASTM committee, but let me guess how this one will play out.
The 3 for 1000sf thing is probably designed to give a good starting point basis for slab temperatures and RH levels. If you were doing an 800sf job and just put in one probe you'd have no other readings to check your one probe against. Putting in three gives you an average and you can see they all jive.
If you have 22 probes in and 4 are in a different area I think you are good because you have that averaging data available. Unless there is a big difference in the slabs (poured on different soils, some are in pans, different finishing methods, thicker slabs, multiple pours on the 4,000sf area, etc.) that's how I would do it.
I always want several probes in to give me that starting point, then I want to check every different pour (cold joints are a dead give away), in corners where the air didn't flow as much, under overhangs, near entry points where water was probably coming in during construction, over thickened portions etc.
You really can
follow the standard and get poor information if you don't think it through. You could technically put all your probes in half the building and ignore the other half and still put in the required number of probes. I think you raise a great question and you are really thinking about the intent of the standard.