The metaNavigation, footer and sectionHeader area definitions in the site definition needs to have an extra property set now: editable=false.

The result of the current migration leaves you with an overall editable metaNavigation, footer and sectionHeader.

Rated as Major since the outcome of a migrated stk site definition != vanilla installation.
However, this should really only be set as a default in the site definition, not to be repeated in a normal template migration.