There are multiple Lugias in the anime.
Another issue with your weird 1 legendary cap is how we're able to pluck other cover legendaries from other universes in USUM. They're not from our planet at the bare minimum, meaning those are still out there.
Solgaleo and Lunala also straight up make a baby that grows into either cover legendary or. Further in the anime specifically this means there's at least 2 Solgaleos.
Arceus HGSS event gets a mention for literally creating a new gen 4 cover legendary.
Shaymin is on the cover of Explorers of Sky so for a lol it's also canonically got multiple specimens in both the main series and anime.
>>48516055>OP mentions anime that's not the early indigo league is fair game>sorry, no anime because it disproves this point immediatelylol