With the next CKM Release, CKM’s Archetype Comparer will no longer report this a breaking change requiring a major revision.
Instead, a change between two archetype revisions where the protocol (or any other top-level ITEM_STRUCTURE) is not constrained in Revision N, but is constrained to something - most likely an ITEM_TREE - in Revision N+1, will be reported as a minor revision [presumed], accompanied with a special tooltip explanation.
This seems to be inline with the discussions above, but if anybody is not happy with this or has ideas for improvements, please let me know.