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.