That's a tough one...they talk about the "Protoculture" theory, but it just means that aliens meddled with human evolution. So they never come out and say it (probably since humans didn't hear anything about Protoculture until Bodolzaa spilled the beans), so yes, it's an assumption. But consider...
1. The APHOS dates from roughly the same period as the Protoculture underwater city (yeah, it's DYRL, so non-canonical, but I bet cities like that were really there in the "real" Macross world as well).
2. Whatever race messed with human DNA also created the APHOS.
3. The Mayan legends clearly refer back to the Protoculture, and also contain references to the APHOS.
So, yes, it's all an assumption, but one which is on pretty solid ground.