So, what are the odds that the Barons are on this island somehow? I have a hard time believing that Scuttle Town would be left alone from danger during Shantae and the FttE's trip if they're all absent from this game.
In any case, so far none of the villains have even bothered to try and find it again or even stumbled upon it, so at this stage it doesn't really seem to matter that much right now. If it backfires, it'll probably be ages before it's even brought up again for starting up another sequel scenario.