Because there is a little-known IETF/IRTF bylaw that no important standards debate can take place without relitigating endianness. You might think I am joking, but I am not. It's Postel's Second Law.
Since X25519 and Ed25519 had already been deployed by a fair few people, all of whom used little-endian, recommending the opposite without a compelling reason would have been a bit too silly. (Upstream working groups are encouraged to consider the field elements as opaque octet strings, to try to avoid arguing the exact same point again.)