No, I think it's in order: they just skipped over the battle in the latest video. While I would agree that such a change occurring mid-battle being unprecedented, I wouldn't discount the possibility entirely. Frankly, shaking things up in the first gym would be a great way to engage the player early on. I admit, though, that they may just appear to congratulate you. (One of the trainers can be seen "hiding" behind the fire curtain across from the grass circle.) Either way, I'm anxious to find out what happens!
Also, from this video:
http://www.youtube.com/watch?v=a1rgd4gozIg&feature=related
"Ms. White!
Prof. Araragi is waiting at the Dragon Spiral Tower at the end of the road out of this town.
Dragon Spiral Tower...where a legendary Pokémon sleeps.
Prof. Araragi is in the process of investigating that legend."
In other words, the "road" might be one through the western mountains, from the Ice(?) gym in Sekka City (windmill town) to Dragon Spiral Tower (white tower) north of the airfield in the west. DST is undoubtedly the same spiral-shaped tower that has been shown in a number of the latest videos.