Yes, Ben, in detail you are correct. I wasn't trying to be argumentative, but thought it was simply relative. They both use similar ECU's much the same internal architecture outside obvious stroke jump to 4.1" which hampers the GT500 on piston speed. But I would think the differences are less than the similarities. Nelson rarely gets aggressive with cams and there again is an advantage with the variable Coyote's higher lift cams and higher cfm heads. So, it looks like if the same perimeters were taken on the Coyote, you'd get even more efficient benefits.
So yes I concur that it would be nice to see what NR can do with the Coyote, but Helion along with others have already shown 1k hp potential. To consider any of NR engines as less than custom/one offs is relative. With what, his simplest turbo 'crate motor" at like $32k and more like $50k for a serious attempt, they all fall towards the custom side. I'm guessing a big enough check would produce a second very similar engine in your garage.