Nah, they aren't same and Game Freak continue to make new traditional main games in near future since Zelda team moved to open world to take advantage of Switch's power, so Zelda sequel will be continue to have open world like BOTW did.
As for Pokémon, there will be multiple series and PLA is considered as alternate main series, so PLA doesn't replace the traditional main games. Pokémon have multiple different games - Pokkén, Mystery Dungeon, Snap, Let's Go, Café Mix, Pokémon Unite, Stadium, Quest, Detective Pikachu and others, but... when compared to Zelda, they don't have multiple different games, so they just go from sequel to sequel.
PLA has much less Pokémon, one town and their map system is similar to Monster Hunter, not open world like BOTW and they are not see as replacement for traditional main games, however Game Freak may use some of PLA element in next traditional Pokémon game, but PLA is alternate and separate from traditional games. I believed that Game Freak classified PLA as main because of storyline since all spin-offs don't follow same storyline as traditional does.
One member claimed that PKHeX isn't going happen and I don't know about whichever member is correct or not, some said PLA is new game with different system and it could take a time for PKHeX to develop or update their save editor, or they may develop own save editor for PLA. PKHeX team hasn't say anything about PLA yet but one thread on PKHeX forum got locked up and moderator didn't say about PKHeX would be updated or not.