So I always thought that when you select 'Edit with IDLE (ArcGIS Pro)', and your ArcGIS Pro PackageManager>Active Environment is set to the cloned environment, that meant it would use the pythonw.exe from:
C:\Users\myProfile\AppData\Local\ESRI\conda\envs\arcgispro-py3-clone\pythonw.exe
Are you saying that is not the case and the IDLE is still using the default environment at:
C:\Program Files\ArcGIS\Pro\bin\Python\envs\arcgispro-py3\pythonw.exe
?