AMA: Enrolling modern devices with Windows Autopilot

That depends. Today, there is no explicit coordination or orchestration between the different deployment methods and so it's possible that conflicts occur because of this. These conflicts are generally unpredictable and thus terribly difficult to discover or troubleshoot. Thus yes, we ultimately recommend that folks avoid mixing the multiple types of app deployment during Autopilot. Packaging your MSI-based apps as a Win32 app is a fairly straight-forward and quick process so avoiding these conflicts is also straight-forward.