A slight sheet metal adjustment would barely cost the teams any more money. The restrictor plate cars are already different than normal ones because of the aero package they use.
I know the Main organizations all have their separate cars for each tracks, but the purpose of the COT was for a team could run a car at Martinsville and take it to Talladega, bolt on the approved spoiler and shark fin(the only thing different) and be able to use that same car. If you change the template of the car, teams will spend $ in the wind tunnel and other types of R&D to figure out how to build a super speedway car that will get an advantage which defeats the plan of keeping the cost down. I agree with you that it would eliminate the tandem draft and the overheating problems, but I just don't think NASCAR would do it.