Well, at the very least, during 1.0 it seems at least that he was considered one, especially as this piece of official artwork of the Primals, which shows amongst other things Odin and Bahamut as well as Shiva, also includes in the bottom right corner, unmistakeably, Good King Moggle Mog the XII.

Personally, because of the existence of that artwork I think that at the very least, until recently the development team actually really did regard him as the Moogle Primal, but, have since changed their minds and retconned it that he isn't actually one, thus confusing 1.0 players and contradicting that piece of artwork.

So why did they change their minds? Well, I guess only Ferne knows the answer to that.