Yes. If allocations are the policy then you'll only be able to order one from your dealer if they have (X) amount of allocated units allocated to them by Ford, and the dealer extends one of them to you. Some dealers will order all of their allocations they way they want them and hope to sell them for a mark up over sticker.
Exactly why I have gone to 5 local dealers expressing interest in building a truck. I will be hitting all 5 the day order banks open.
If you know a dealer well enough you can get in line for one of their allocations and then they will change the way it was ordered for you to match your preference. But that can only be done up to a certain point in the order process.
Went through all of this crap last year when I ordered my GT350. I know it won't be an issue this go 'round for me, but it shouldn't be nearly as big of a PIA to order a Raptor.
Only way around the allocations is that your dealer can trade for one. But it has to be on the lot first. So at first, good luck with that. Still not a bad idea to let them know to keep their eyes open for one.....