I agree that runtime algorithm negotiation makes sense to avoid sometimes. So just make a spec that factors out the algorithm, and make the choice of algorithm a compile-time thing.
Then there's no need to hardcode anything in the spec, you can just say you're using the protocol RFC-12345-ChaCha20Poly1305 — with RFC-12345 being the spec that leaves out the algorithm.
Yes, that's pretty much what I meant by "standardized". You'd be able to pick AEAD cipher, KDF, signature algorithm, KEX algorithm etc., while the spec would only describe the protocol itself without enforcing specific algorithms. Noise Protocol pretty much does this already: you provide a string that describes the set of algorithms you will be using, e.g. "Noise_NN_25519_ChaChaPoly_BLAKE2s"
Then there's no need to hardcode anything in the spec, you can just say you're using the protocol RFC-12345-ChaCha20Poly1305 — with RFC-12345 being the spec that leaves out the algorithm.