Yes, tileAt: is here. If you scroll down, you'll also find version that'll give you the tile GID without the (flip) flags, or just the flags. No need to bitwise "uhm" them ("uhm" as in: what was that bitwise operation again that clears the flags?).
To get there you would first get a reference to a TKTilemapTileLayerNode which exists as child of the TKTilemapNode. Said layer defines the layer you want to get the tile from, and TKTilemapTileLayerNode has a reference to TKTilemapTileLayer with this function. Right now it's strictly OOP but I'm absolutely okay with moving often-needed functions to where they're used, in this case the TKTilemapTileLayerNode itself.
A Cocos2D version will certainly be available. I'll launch the beta with Sprite Kit first though, and very soon. Following that I will try and launch a Cocos2D beta after that, I'm just a little unsure regarding how I can make the framework behave nicely with all the different v3 versions already available (it shouldn't crash or cause compile errors). Maybe it'll turn out not to be an issue after all.