Yeah, switching operating systems is not expected to be automatic (I hope we haven’t given the impression anywhere that it is). They aren’t the same in a lot of ways; Virtualmin and Webmin paper over a lot of those differences, but there are still some pretty significant things done differently under the hood.
It shouldn’t be a major ordeal to migrate, but, you also should not expect it to be done in an hour or two and without some reading/testing.