Microsoft 365 features that help users manage their subscriptions, account settings, and billing information.
Hello Tim Bernhardson1,
Good day! Thank you for posting to the Microsoft Community. We are happy to help you.
Based on your description I understand when registering multifactor authentication for a user you can only see the option for app and phone but more options are enabled in the Microsoft 365 admin center. To troubleshoot this issue kindly open a service request in the Microsoft 365 admin center Get support - Microsoft 365 admin | Microsoft Learn, the support team there can help you remotely to check the issue and they can collect logs and investigate the issue from the back end.
We look forward to hearing from you. I appreciate your cooperation.
Sincerely
Microsoft Community