I wouldn't say the game goes against its lore more like the lore is evolving. The world never stays the same, and in an MMO I would think the same thing. As for the inconsistencies of the primals I have my own theories on that.
Mostly we are lead to believe, even within the games lore, that the beastman tribes were made by their respected primals. However, my theory is that isn't true, kinda.my thoughts are that the primals didn't create the beastman, but the other war around, that the beastman actually created their primals, I'll explain. Currently, the races of man revere/Worship the Twelve, and mostly we've been told they actually existed, but were normal people. Now for the beastman, what if a similaf thing happened but to a greater extreme. The beastman tribes had a "hero" that after their passing they revered. But over time that reverence, or rather the reason for that reverense was lost and they began to worship that "hero" as a god. Well, now that they have the powerr to summon their god, their prayers that they had already done for so long actually give them form. In this sense the beastman actually created their god through reverence. Think of it like real world religions, like Christianity. It's said god created man, but we have no proof of an actual god existing, so by that sense we actually created the god we say created us. The same could be said of the beastman, regardless of a hero ever existing or not. And the newest Primals of Mog and Shiva actually support this a little since unlike the other Primals whose histories are a lot older their histories are relatively recent, enough to know that they did exist, at least in the current time line. Possibly in the future they'll exist in the same sense as all of the other primals. Of course this is only my theory, though I would like to think it holds some merit.
And as far as Midgardsormr is concerned, it's been hinted that he is a god/immortal, and was just born into a mortal form at one point, but since the player/scions didn't know this it makes sense they would just think he was dead. But this is only hinted at so if it's true or not remains to be seen.
