Hi @Alex Wilber
Thank you for posting this in Microsoft Q&A.
I understand your concern that you don't want Phone and App password as second factor when registering MFA and want the method 1 is app and method 2 is Email.
You can use Authenticator App is for two factor authentication and password reset authentication. The email method is not suitable for two-factor authentication, only password reset is supported.
If you are using Legacy MFA follow below steps:
Security > Multifactor authentication > Additional cloud-based multifactor authentication settings > Verification options > Select Notification through mobile app and another option.
Password reset:
1.Need to select users for SSPR.
Protection > Password reset > Properties page, under the option Self-service password reset enabled, choose users according to your requirement.
2.Select authentication methods.
Password reset > Authentication methods > select two methods i.e. app and email.
For your reference: self-service password reset
Hope this helps. Do let us know if you any further queries.
Thanks,
Navya