If they made the STi trans and diff an option in the WRX and made the STi suspension setup a standard feature then they could focus on building one car, which would save money in a few different ways. Currently the only reason to buy an STi this year is for the bulletproof driveline and its outstanding trackability (if that makes sense), which most buyers will never need (just my opinion). Having that Diff or Trans as an option on the WRX would kill the STi sales so it just makes sense to focus on one platform.
It could very well end up becoming how US automakers run things at times. Have 1 car and a short list of driveline choices and maybe a sport tuned suspension option (and a wingless option hopefully lol). Saves on money on marketing that's for sure.