The best case would be for NIPs to be fully atomic. If a new NIP changes or replaces an existing one, that should be clearly indicated. The existing NIP exists for legacy purposes, but is clearly marked as deprecated so new development work focuses on the current preferred implementation.
That's basically how the existing web works. It takes a long time for changes to get to everyone (remember how long IE11 was supported?) but it ensures a consistent experience for older software.