You can always order a car from a dealer. Advantages are getting exactly what you want; disadvantages are having to wait.
Also, Ford has allocations for popular models, to make sure one dealer doesn't grab them all, and get them to the places that actually sell. I doubt you'd run into this with a Focus, but it's possible. Maybe the ST, right now, since it's just starting to be produced.
Dealers usually prefer to sell stock they already have in inventory, if for no other reason than they've borrowed money to stock it and they're paying interest. So you might have to twist their arm to place the order.
The reason most people that ordered their Focus ST months ago are still waiting is that Ford is just now (Oct 1) beginning to produce the ST3 variant (the 202A options package). There's a backlog of preorders from before the car was in production at all that they have to work through.
Even under good conditions, 8 weeks is not an unreasonable time to expect to wait if you order a car.
It's good that you can walk away. The ability to just say no is your best negotiating tool with the dealer.
I'm not a moonroof fan either, and I've seen exactly zero of the initial round of ST2s come out without a moonroof. Guess that's just what Ford chose to build in the first wave.