>>36949335The franchise takes its plot relatively seriously considering what it is, so there's a suspension of disbelief insofar as the events in Kanto, especially w/r/t Team Rocket, repeating themselves ad nauseum.
This is completely baseless speculation on my part, but I would not be surprised if the Giovanni of LGPE is suggested to be the Giovanni that forms Rainbow Rocket, and is not the same Giovanni that Red defeated.
That's to say nothing of the contradiction insofar as the Fossils at Mt Moon regenerating, two additional Snorlax presenting themselves as blockades, the Silph Co scientist giving away Lapras to both Red and LGPE's protagonist, etc. but these are on a smaller scale of continuity breaking.
I think I get what you're suggesting – that dialog after the fact retconned Red's story to something else entirely than what we played in RBY and it was in fact LGPE's MC that takes down Red, and not Red, but does that really make much sense? Then how does Red defeating Blue to become champ fit in? When was Blue champion, and when does he take over the Gym? The only way to fix the plotholes is convoluted headcanon.
(ORAS has the same problem. A few lines of dialog here and there are meant to be nods to them being remakes of 10 year old games, but suggest RSE happened, and then ORAS happened 10 years later.)