Well, if that's their reason, they don't have a reason. I was able to make ME1 and ME2 work with my 360 controller flawlessly, using their UI exactly as it's intended for the PC. If I could do that using a 3rd party emulator program, it wouldn't be much for them to build it in.
I suppose I could just do it again for ME3, but it takes hours upon hours to build a new profile from scratch and get it to work just right.
Or they could just make two UIs like some companies do. Though like I said it was a Bioware non-answer so who knows what their real reason is. Bioware is rarely forth-coming with full answers.