When I try to connect to Dynamics 365 CRM with the Plugin Registration Tool I get the following permission error:
"You don't have permission to access any of the organizations in the Microsoft Common Data Service region that you specified. If you're not sure which region your organization resides in, choose "Don't know" for the CDS region and try again. Otherwise check with your CDS administrator. Parameter name: EMEA"
Solved by leaving the "Show Advanced" checkbox unchecked and not entering User ID / Password. Then a second dialog opens for credentials and 2FA authentication which just works.
You don't need an application password, as you'll be asked for MFA in the next step.
I don't know how our old teammate was able to sign in with the "Show Advanced" option selected. He was getting the same dialog and continue.