It’s clearly supported as evidenced by the presence of the feature.
However, as a desktop user wanting to upgrade the same machine frequently, you’ll find (as you already have), that it makes the upgrade procedure between releases a bit more involved.
I’ve seen several people mentioning that they keep a script around so that they can to a rpm-ostree reset first, then run it (with minor changes), to set the layering up the same way again on the new version (maybe after changing the version for their rpmfusion repos or whatever).
Personally I have very few layered packages, so I’ve generally just kept the rpm-ostree status for the previous version before upgrading, then use that to reinstall the same list of packages afterwards. Right now I have 16 layered packages and no other overrides, so it’s pretty manageable to do a couple of times a year.