Hello @LeRoy, Kevin,
There are no risks and limitations if you use the same methods that are used in the legacy authentication methods policy in the new authentication methods policy.
Replicating the legacy policies with the modern authentication method policies would not have any effect on guest user access, email OTP and External user workflows.
You can definitely use the 6-digit code, but you need to make sure that the software OATH tokens method is enabled for the users in the modern authentication methods policy.
If you do not want to use Push Notifications but only like to use 6-digit code, you can do this by disabling Microsoft Authenticator in the MFA policy but enabling software OATH tokens as an authentication method. Also please make sure that you disable the registration campaign which enforces for push notifications.
https://learn.microsoft.com/en-us/entra/identity/authentication/how-to-authentication-methods-manage
Managing Security Questions is not yet available in the modern authentication methods policy blade, but you can complete the migration and still use the Security Questions but any changes to this method must be done from the SSPR page, but you can still use them after migration.
Please make sure you enable the security questions method in the SSPR blade before migration itself, and this method stays on this page and there is no concrete information that this method would be moved to new authentication methods policy page.
I understand that this is a big move to migrate from legacy to modern authentication methods policy but if you enable the same methods and replicate the legacy methods policy to modern methods policy the end users would not have any impact and will have a hassle-free experience.
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