I worked at a dealership for 11 years, and I don't remember us charging to trade with another dealer. Or at least, we may have tried to but if someone said they weren't going to pay it we weren't going to loose a sale over it. The only way I could see them charging you to dealer trade is if they're trailering the car to you rather than sending a driver to pick it up. Little more work involved with using a trailer, and even then I would bet they'd waive it if you really made a stink over it.
It sounds like they're really trying to get you to buy one that's already on their lot. No harm in that, as it's easier for them, but if you're buying a new car make sure you get the one you want.
I ended up doing a factory order on mine because: 1, I've always wanted to factory order a car and get exactly what I want and nothing I don't. And 2, while they offered to get one from another dealership, I'd prefer the car to have as few miles on it as possible so that I know how it's broken in.
Of course, it helped that my dealership hadn't had a BRZ on their lot in years, so it wasn't like they were trying to get me to buy inventory they already had!
