This is news to me; do you have those sources on hand?
The only thing I remember from reading interviews was that the presence of Phoenix's aether in the Calamity (alongside Bahamut's) was why we were able to attune to them, nothing about that being related to the three egi limit or us having technically gotten Bahamut and Phoenix as Egis
before getting the other three. The whole reasoning with the Trance was specifically to get around the Egi limit.
(The interview I'm referencing is this one; I don't know if it's the original, but has the explanation about Phoenix
https://www.4gamer.net/games/199/G019924/20210810055/ )
This is meant as an honest question, I should clarify, I'm not trying to make some accusation that you're lying. I just never came across that information, and I've been generally frustrated by the lack of given lore explanation for why we can summon Bahamut and Phoenix egis despite the limit. If the devs have actually answered that question, I'd definitely like to finally have the answer (even if I'll admit I don't particularly
like the "we already had egis in us" answer, it's at least an actual answer!)