Couple days late, but since it's my several year old thread that was bumped I'll post up lol
Definitely sounds like that ford dealership doesn't know raptors, if you have OEM SVT suspension and they're saying it's aftermarket. It's no surprise though, the dealer that my Raptor was courtesy delivered to when I bought it was all confused that it showed up on the same transport as other vehicles from the train yard, they didn't know how that happened because they kept telling me that ford builds it as a regular f150 then it's sent to fox to convert into a Raptor lol. Amazes me how uninformed many dealerships are on even the simplest details.
That off road shop is taking you for a ride. 600 is wayyyyy too much. You need to compress the spring, slide the collar up to the next perch, and align it. It's nowhere near 600 in labor. They're charging you for a lift kit that you don't need because the adjustability is built in from the factory. It's been a long time, but I think I paid around $250 or so from KHC with alignment. $300 or less it's a no brainer if it includes alignment. Double that is just the shop ripping you off. Keep hunting, there's definitely gotta be raptor friendly places out by you in CA.