A minor note on terminology and a caution on how to treat Final Fantasy lore in general. Never, ever, ever presuppose that an assumption that holds in one Final Fantasy game will also hold for another game. The use of the word Prime in FFXI was significant in that game, but there are enemies in other games which use the word Prime in their names that are nothing to do with that - notably off the top of my head is Cactuar Prime from FF13, which was not the "Prime" form of the Fal'Cie Cactuar as one might expect using the FFXI definition, just a really strong Cactuar.
That's not to say that your theory doesn't have some merit but apart from Bahamut Prime and Atomos Prime we have not seen any other "Primes" in the storyline, and given how important Primals are in FFXIV, I am sure they would have appeared by now, and their first appearence would not have been in 1.) the hardest battle content in the game, and 2.) an optional side-story questline based on FFIII. As far as Atomos Prime is concerned ... I thought it might've been a graphical glitch that I did not see a giant Atomos we were fighting but apparently it is not. But if Atomos Prime were the "Prime" Atomos ... is there any evidence (Other than Egi which are slightly different) that any primal can be summoned more than once at any given time.
I have other things to say about Primals, mostly to do with gestalt psychology and collective conciousness but I'll leave those thoughts for another day.
