Many engineers aren't good bean counters. I know because I work with them daily. The team of engineers on the Mustang is huge and they are each given a task of designing a widget. Then there's another set of engineers that makes sure the widgets all work together to make a working car. An engineer can't know everything related to a cars expense like wages, overhead of the facility etc. The accounting department tracks these things and they are like the ones that really compute the true cost. The marketing people determine as much about a cars features as the engineers. They determine market demand for everything from price to horsepower to paint colors to options and standard equipment. Then they tell the engineers what specs to shoot for in their design. Engineers probably have very little to do with the overall look of the car. That's probably determined from focus group input more than anything. Engineers also don't negotiate price with Fords vendors, UAW contracts, etc. All these things impact a cars price. The engineering process is just one of many variables that effect final cost to the public.
Ford may offer this in the future if the demand is there. I would wager they have determined the cost of offering the IRS option and it is prohibitive. If they felt it was a profitable item then they would offer it. How much would you be willing to pay for an IRS option on a GT or base Mustang?
This is called marketing. There's nothing wrong with Ford making limited run models and charging more for them. That is capitalism. If there isn't a demand for these models then they are discontinued or the price drops until they sell. If there's a public outcry about the lack of an IRS as standard or an option then I'm sure Ford will respond accordingly. From the posts in this thread I would venture they would hear more complaints if the live axle was dropped.
Marketeers are the ones that formed the 2005 Mustang to be what it is. Without their bless the new car wouldn't have seen the light of day. I like to give credit where it is due and Ford's marketing department deserves a lot of it for the final form of the new Stang, IMHO.