Where do you have the information about how Wireguard would handle such a transition from? Looking at https://www.wireguard.com/protocol/ I can see no protocol version or other means to distinguish between an old and new version of the protocol. Also this would introduce additional configuration and a negotiation step which seems to run counter to the motivation of the project.
Not preparing for for this inevitability seems foolish which leads me to believe that this was not an oversight but a deliberate design decision by the creators of Wireguard.
 Page 10 onwards of https://www.wireguard.com/papers/wireguard.pdf
Also looking at the struct it seem the three bytes are only reserved in order to align the following fields on 4-byte boundaries.
If the authors had the intent to allow for some kind of asynchronous update path then surely this would be built explicitly into the protocol right from the start.
Fortunately I know exactly what I was thinking. Each message has an explicit type. The set of types exists in the first byte with the remaining three reserved for future additional use, perhaps for naming types. The cryptography is tied to the version by way the identifier and construction constants.
Regardless, it is clear that there are numerous ways that can be backward compatible to extend wireguard into v2. IIUC, the deliberate design decision is that "we are not baking any specific one-true-way". It's not "not preparing for the inevitability", it's "the way protocol agility has been done so far has failed, we defer this decision closer to the time we need it".
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.