I wouldn't read too much into Vivillon's "secret". See: Pattern Bush, Underground Tunnel Celadon-Lavender, Ruins of Alph...
We've had plenty of instances where the supposed "secret" turned out to be simple lore. For instance, the games explicitly state that there is a lot of unsolved mysteries regarding Pokémon eggs (for starters, no Pokémon has ever been seen laying an egg), but it is of no importance to the games.
Also, Swoobat and Noivern have as much in common as Golbat and Gligar. They are both bats... ish, but the typings are different, the themes are different, and any similarities in appearance is just coincidental.