Assuming the faucet is mounted through the deck, yes, you'll want to tile that first. Often, it works out well if the pipe is left long and then cut off when physically attaching the faucet you ensure the pipe is properly oriented in the hole through the deck. You can cut the hole after the tile is installed, bit if things skate a bit, you might scratch the tile up, requiring it to be replaced. Just make sure there's no blocking or joists where the plumbing needs to go, or you can mess things up or keep from being able to tighten the nut or whatever they use to tighten the valve in place. One way to help alleviate that is to make a template with a piece of plywood with the holes where you want...fasten it to the deck with some strong tape or clamps if you can, and use those holes as drill guides for the diamond hole saw.
Assuming the tile are larger than 2x2", you could use Ditra on the deck of the tub, then install the tile on that. That would be about the thinnest installation as it can go directly on the plywood decking, minimizing the buildup, and if you use KerdiBand on any seams, would make the deck waterproof. You could make your entire tub deck out of KerdiBoard, and get your waterproofing in one step. KerdiBoard would be too thick on the top for your valve, so the easy way to resolve that is to use a router in the panel with an overlap of about 5-6" around the holes you need, route a pocket in the foam, then embed a tile so that it's flush with the top of the board using thinset underneath. Once that cures, you can cut out the foam below large enough so you can then clamp the valve to the tile section after you've tiled the whole deck.
