How do you enroll iPhones in MDM? DEP, User Enrollment or good old profile enrollment via m.meraki.com? We have had O365 with MFA and MDM for a couple of years now, never had any problems. What kind of restrictions, settings and credentials are you pushing with your profile?
As mentioned below Outlook is a preferred option here, but our users use native Mail as well. It does sometimes require mail account reset but it has nothing to do with MDM and happens on both enrolled and not enrolled devices.