I don't think it's obvious that they should naturally be allowed to prevent a clean-room reimplementation. The real innovative and creative work is in the designs that would be protected by copyright - the alleged "innovative circuits" subject to patent are really just being used as patent traps to prevent a clean-room reimplementation of the architecture - as anti-interoperability measures, in other words.
I don't think it's obvious that they should naturally be allowed to prevent a clean-room reimplementation. The real innovative and creative work is in the designs that would be protected by copyright - the alleged "innovative circuits" subject to patent are really just being used as patent traps to prevent a clean-room reimplementation of the architecture - as anti-interoperability measures, in other words.