I'n not sure I understand the difficulty with your two airport scenario.
I'm assuming A and B have the same QNH, so the surface pressure is the same at each place.
With an acccurate QNH set at A, you take off at 100' amsl, climb 900 ft, and now you are at 1000' amsl. Your altimeter reads that too. It has gone from 100 ft standard pressure to 1000 ft standard pressure.
Now you fly to B, using the altimeter to maintain height, i.e. maintaining constant air pressure. As the air beneath you becomes less dense, you need more of it to maintain that pressure, so you slowly climb to, say 1080' amsl. Your altimeter still reads 1000.
Now you land at B, so you descend 980 ft (from 1080' amsl to 100' amsl). Your altimeter measures the increase from 1000 ft standard pressure to 100 ft standard pressure, so it shows 900 ft less, not 980 ft.
The pressure decrease at A equals the pressure increase at B, so the altimeter winds up and down the same amount at each place.
In standard air at A you needed 900 ft to do it, in less dense hot air at B you needed 980ft to do it.