It appears to me the default environment arcgispro-py3 is in a bad state.
First please try this to confirm:
From Python Command Prompt, run the following:
conda create -n arcgispro-py3-test arcpy
proswap arcgispro-py3-test
conda install <x> <y> <z>
*<x> <y> <z> are placeholders for the packages you want to install, replace these with appropriate package name(s).
Are you still seeing the inconsistency warnings?
If so, could you try uninstalling Pro, then make sure that %programfiles%\ArcGIS\Pro\bin\Python\envs\arcgispro-py3 is completely removed before re-installing Pro? After this, it should be back in a good state.