>>36308001From my understanding, FRLG is Gen 3 despite being a Kanto remake, so here LGPE is being Gen 8 (or Gen 7 or Gen 7.5 since apparently the 2019 games are going to look different). That being said, LGPE having Megas show up again is equivalent to Gen 7 having Megas show up again is equivalent to previously introduced Pokemon showing up in later gens, Lucario showing up in Kalos in Gen 6 for instance. I know they did Pokemon: The Origin to have Megas a part of the game as well, Mr. Fuji does say it was a tradition passed down from the Kalos region, rather than being something additionally inherent to Kanto and potentially other regions.
tl;dr: Megas showing up in a later gen is already justified by Pokemon traditionally showing up in gens/regions they're not introduced in
