I installed a corner Better Bench in my mother's shower. They advocate either installing it on top of the tile, or to the wall, then tile around it. I opted to tile first, then install the bench since there would be lots fewer cuts. This means drilling holes through your tile and waterproofing the hole, which needs to be done with care. It's easier if you installed blocking first, since your holes will be smaller. It feels a little flimsy until you fill it up with deckmud. I found that you needed to be careful trying to get the corner bench to slope properly since it appeared to be essentially built without that slope (wouldn't be an issue on a bench along one side or the back wall and a side). I suppose you could slope it only against one wall, but I wanted it to slope from the corner. I didn't feel comfortable trying one that was entirely cantelevered which is why I chose a corner one (although I could have used a rectangular one). The corner one was enough space, and it didn't impact the size of the standing area as much. When thinsetting on the tile, the edges are a little tougher, since the thinset will only get a really good bond to the deckmud that is exposed by the holes in the metal seat...it will bond some to the metal, but most of the bond will be to the deckmud, so careful burning in of the thinset is critical. There's no problem with the top since it is all deckmud.
If you want to make a box, then you might consider KerdiBoard or WediBoard. That could be tied directly into the waterproofing of the shower more easily.
It's best to have a steeper slope when using river rock or pebbles on a shower floor verses tile. While some thinsets might be okay, most are not designed as an exposed, wear surface. They tend to be more porous, and would collect more crud. There are some grouts that you could use to set them, though that would avoid that problem.