Currently as of build 4.16.3.288 MNE does not support Multifactor Authentication.
Multi-Factor Authentication requires periodic approval for Office 365 sign ins. MNE is designed to start a migration immediately, or via a scheduled operation. Once the migration is initiated, MNE is designed to not require any further user interaction. MNE is designed migrate multiple users in batches and may login as a new user at anytime. If MNE had to wait for login approval, then this would essentially stop the production migration, especially for migrations occurring during off-hours.
