I just figured Alto Mare was something the anime staff came up with for an interesting movie setting since Venice is cool. (I've been there, can confirm.) It's not like the games ever directly reference it or allude to anything similar for Lati lore afaik, and specific ties to the anime have never been consistently applied anyway.
Specifically the Latis spend a lot of time underwater rather than flying around in the movie.
While normally I'd agree that the anime wouldn't have any impact on a Pokemon's learnset bar very deliberate events and such, M05 did release about 3 months before RS did which is definitely long enough that storyboarding and movie planning could have impacted the learnset process while developing the games.