On the one hand, this ups the odds that Baldur's Gate won't be in turmoil from a nautiloid attack. Which is good in my books. On the other hand, if we weren't taken from Baldur's Gate, how does that square with our player character pote tially being from there? Will we get to acknowledge why we were in Yartar? Because the cinematic heavily implies that we were taken from there. Or is it just going to be the case that our kidnapping won't be acknowledged?
Our character isn't always from Baldur's Gate. Not all of our companions from BG and looks like only Astarion was kidnapped there and it's still not clear if he was taken directly to the Nautoloid or dragged out of the city first. Shadowheart was on her mission somewhere, Wyll says he was kidnapped while camping. The rest are not baldurians.
For all we know it's either baldurians are somehow preferable targets for the Absolute or it's all just a funny coincidence or our character being baldurian is just a placeholder.