Everything else is the same. There's discussion here and there that headstock shape/size makes a difference in tone, but if that's true, you couldn't prove it by me. People hear what they want to hear.
When I first started doing it, it cost $45 for the work. Today, I think they want $60.
There's no difference in cost between a Warhead and Strat headstock if you price one up from scratch. But, the selection in the "Showcase" of nearly ready to ship Warhead necks vs. Strat necks is dramatic. They make a LOT of Strat necks, so the chances of seeing something built on spec that just has you touching yourself in anticipation are much higher in the pre-built Strat selection than the Warhead selection.
Cost-wise, you have to bear in mind that Showcase necks are about 10%-15% less than custom pieces you call out yourself. So, the upcharge to have a Strat headstock re-cut is usually a matter of expediency rather than cost savings. If the neck already exists, it only adds maybe a week to delivery out of stock, while having something made from scratch could be anywhere from 4 - 8 weeks, depending on finishing options. In the end, recutting an existing Strat neck puts you roughly at the cost of custom ordering a Warhead. In other words, recutting a showcase Strat neck costs about the same as a custom order Warhead, but you get it faster and you get to see what it's going to look like before shipping.