So sorry I let this one slip by without posting an answer.
You said in you OP you can't get PF3 to give you 'Altimeter' instead of 'QNH' yet your log shows differently
30/11/2021 23:36:25: 840 - Transcript: 'Redair Papa Hotel Mike Juliet Victor Readback correct. Altimeter is 997 Report When ready to taxi '
With regard ATC nagging you about your altitude there are a couple of things you can do. Personally I just fly a few hundred feet higher or lower. You could of course turn the ATC nag off in options. This problem is caused by FS2020, for which everyone is hoping there will be a fix from Asobo at some stage.