You're way over thinking this. Maintaining the stock height is a good thing for the street but isn't necessarily the best thing for the track. Lots of guys are running 18" wheels for the track which allows you to put lighter wheels with more rubber and get the car lower to the ground. The race cars run 18" wheels because that's what their spec classes call for and the availability of race tires. Ford did a great job with our cars for meeting their internal requirements for driving on the street but there's plenty of room for improvement at a cost, both money and ride quality. Read below for more info. And for the life of me I can't figure out why Ford didn't put 10" rear wheels on the Boss. Maybe just to have one more item different on the LS.
Ford Racing Suspension Upgrades
I'm thinking you are right about the one more thing different from the LS. I really do not see why they would have done this either.