SPOILER
I was right there with you, right there with you almost all the way through. I was just waiting for an explanation of what the flip was going on with Echo's special ability ... I was waiting for the explanation for that and it just never came.
I feel like it could have been completely justified if the explanation for Ultimate Memory had been something else -- like, this only even requires a change in Gaia's dialogue at one point. There's already another Ultimate with science-violating powers (Ultimate P. from the Epilogue) so Echo being (ROT-13 encoded) Hygvzngr Cerpbtavgvba wouldn't break the story and in a cockeyed kind of way it fits with "Ultimate Memory."
(Yes, they did it in Zero Escape, but it made sense there and it was the central conceit. It didn't just, like, happen.)
I am also *completely* in the dark about what's going on in the post-credit flashback.