They 'could' have, but look at the 800 standard cars; They're from GT4 and GTPSP. If they removed the car variations like this there would only be around 500 standard cars not the estimated 800. It means they're still counting them as seperate models, and including them as 'trim' options would complicate the buying menus. And a lot of people on here have voiced their opinion that the simplistic GT3 menus were better the the over-complex GT4 menus. Though I personally would welcome what you are saying, a lot of people would hate that idea.
The best indication we have so far about trim options being included is one of the demos which showed the SLR Mclaren 19" wheel option on the race menu screen.