According to the Extra-Terrestrials article on Vault Wiki, The Shi Emperor apparently made reference to Extra-Terrestrials.
The Shi computer never specifies what it's referring to. Since the ET aliens are basically non existant at this point, in that there's only one encounter with them, and it's dead, it's more likely it was referring to the Wanamingoes, which are actually in San Fran on the tanker. It's important to note what Xeno actually means.
Main Entry: xen-
Variant(s): or xeno-
Function: combining form
Etymology: Late Latin, from Greek, from xenos stranger, guest, host
1 a: guest : foreigner b: that which is not the host
2 a: strange : foreign b: not being the host
http://www.merriam-webster.com/dictionary/xeno
It doesn't necessarily mean alien. Without more input, one cannot state certainly that it was an ET they were referring to.
There are many people credited with contributing to FO2. I assure you that the wanamingos were not a product of a concerted effort from all of those people. I think Avellone's contributions were mostly limited to New Reno. I can't imagine that he created the wanamingos considering the fact that he obviously doesn't care for them and he couldn't even remember basic details about them (like the fact that they had a queen).
Considering how many things they wrote for the game, there's going to be huge amounts of data, and being that he's human, and not a computer, it's entirely possible for him to forget a detail here and there. In any case, since the bible was written while he was still at Black Isle, with not only his knowledge, but the design docs, and the other devs to confirm details with (which, I do recall he did so during the compilation of the bible on some subjects). So if Avellone says Wanamingoes are NOT aliens, and that they are forever dead, then in the Black Isle Fallout universe, that is exactly the case for them.