Yes, Migration Manager for Exchange supports Modern Authentication.
Product Update 20200824EX
This release introduces the following features and enhancements:
- Migration Manager now supports scenarios supported by MAgE for migration to Microsoft Office 365 tenants where Basic Authentication is turned off. This change is intended to support disabling Basic Authentication announced by Microsoft. By default, the Modern Authentication (based on OAuth 2.0) only will be used after this update is installed.
IMPORTANT: Please consider, after Basic Authentication is deprecated by Microsoft, public folder synchronization by legacy Exchange agents will no longer be supported. We recommend that you start using public folder synchronization by MAgE instead.