Roush staying away from the engine and transmission on the Raptor could mean any number of things... from "this thing is already on the edge and we don't want to tip it over" to "we don't have the expertise to tune this engine/transmission" to "Ford Performance is going to release a line of performance upgrades for this truck, and we don't want to step on them"... or any number of other things.
A buddy of mine worked for Ford Performance until about a year ago, and hearing some of the info that he had to offer (remember the old Paul Harvey segment "The Rest of the Story"?), it wouldn't surprise me a bit to learn that there's more to the story of why the Roush Raptor is what it is (and isn't).