I rather put my stack into the best currently known crypto rather then a highly complex cipher negotiation process.
Having said that I still would have preferred for something like a single increasing integer as the "cipher suite version". This would have allowed for the option of updating Wireguard asynchronously on both ends without any additional configuration or cipher suite coordination with the peer.
This already essentially exists. If the first byte of an initiation message is 0x1, then it means you're using "Noise_IKpsk2_25519_ChaChaPoly_BLAKE2s" "WireGuard v1 zx2c4 Jason@zx2c4.com". It seems like this thread is going in circles based on incorrect information about how the thing actually works.
Have you considered mentioning the way you intend to deal with cipher breakage/deprecation more explicitly on the Wireguard page?
Why does the "increasing integer" matter to you? In what way is it better than "I am willing to protocol 1, 4 and 7" (implicitly "but not 2, 3, 5, 6, 8, 9, 10,"...)? And the "I am willing to .." is just a successful handshake. You try in order of preference; If you succeed, other side supports it. If you don't, you go to the next one. Wireguard does not produce a response unless to a non-confirming attempt.