The thing is, a director like Scott, at this point in his career, is going to basically come in and do whatever the f**k he likes, with zero regard for franchises, canon, or other marketing terms (which is explicitly what these ideas are) that might limit his creativity. And he's done it twice, for better or worse.
This is literally a chicken/egg scenario, where Scotts answer is that the egg, in fact, came before the chicken, since it was made in a lab. David made some eggs, and he'll eventually make a hen that can self-perpetuate the eggs.
You don't have to like it, but that's how it is, at this point in time. On the other hand, you could choose to ignore Covenant until something in the future retcons its retcon.