Although I'm a lawyer and not a builder (my sole effort was an abortive attempt to build a Jeannie's Teenie in the late 60's, abandoned after several of them crashed), but I don't think that the extent of modification has any effect on the legal status of the aircraft. The FAA doesn't care what you call it--they're all Experimental to the FAA. Since a builder only has to satisfy the FAA in terms of registration, it wouldn't matter how much or little the plane has been modified as long as the FAA inspectors are satisfied as to its construction.
In terms of the builder's relationship with RR, that is governed by the relationship (i.e., whether they have a contract). Any complaint RR may have about people building a KR or claiming to have a KR would be strictly between the two parties. Without a contract with the builder or owner, RR has no influence over either. Further, one can call his plane a KR with or without RR's approval or registration as long as it isn't done for an improper purpose (such as defrauding a buyer), although there might be some liability for misrepresentation to the buyer if the modification rendered the aircraft of less value than a plans-built KR. Considering that almost every (if not every) KR is modified from the plans to some degree, this would be a very difficult position for the buyer to maintain. Max Hardberger