Thanks for investigations! Indeed, we do change byte order when storing/loading private key, as MPI should be big-endian, while curve25519 private key is little endian.
Do I correctly understand that we should store it in the MPI as it is (like with Ed25519)? It would be nice to clarify that in the RFC draft.
Another thing is that in my test even if byte order is not reversed in the secret key (including the attached test key), GnuPG still asks for password, reporting "error sending to agent: Bad passphrase".