SVT is just a badge, it doesn't really represent a crack team of engineers. It's more of a symbol representing a "team" of dedicated Ford resources, engineering, marketing, styling, planning, etc... that worked in concert to make these niche vehicles happen.
The engineering backbone for SVT was SVE, headed by John Coletti. Knowing the huge timelines that new models follow, Coletti probably had a huge hand in the decision-making on the GT500 prior to his stepping down, with the car largely "done" and only testing and refinement and production-tooling/processes remaining to be completed.
The SVE skunkworks under Coletti was located within the Danou Tech Center, space that was shared with Roush, where a ton of drivetrain development, and research, and testing, took place. I have no idea what the relationship is currently, but it's no mystery that SVE and Roush had a very close working relationship. Realize that Jack Roush is involved in MANY areas, some more public than others. He does alot of O.E. outsourced engineering and testing, which as zero-to-little relationship to Roush vehicles, or racing ventures, etc..
I wouldn't be surprised if Roush did alot of the hardcore engineering on the Ford GT driveline, per SVE's directives and oversight. But I'm speculating, it would just make sense though, given the fact they shared that large space together, and worked in concert with each other.
To say that Roush engineered it et al may be giving them a bit too much credit. I think it would be more likely that SVE was the architect, and Roush was the team of "architectural drawers and designers" that worked for and answered to the architect.
All of the heavy engineering and testing documents I've ever seen for the Ford GT were generated by Roush, but that's driveline ONLY.
Saleen was more involved in paint/assembly, with final assembly taking place by Ford at Wixom..