Its not meant to sit flush, if it did it'd be too far away, also its as flush as any other HU, as the screen has been grafter onto an double DIN adaptor...
I know how and i would't say it was easy, there are allot of pitfalls associated with putting a PC in a car, mainly the HUGE risk of interferance...but it is worth the effort and money spent, i havnt seen anything else that offers similar functionality with the same flexibility...
I don't know about yours but when I had a double DIN touchscreen unit in my car I Could pretty much never see the Screen (in day) because of the glare, which for me just rendered the whole thing pointless so I got rid.