Appears that our ConfiguratioInterfaceImportData was not saving the schema version. Thus, it resulted in schema updates even if the version of exported profiles and environments are in correct and current version. We need to add schema version to the import data as well.
This still does not remove problem from previously exported configurations and can not be fixed. But users could manually add schema version number to the ConfiguratioInterfaceImportData as it's anyway written in all exported data and thus available within the exported file.
In order to reproduce:
Import the same one