I was thinking that if you added illumination you could keep the buttons white, and the display red so it would sort of match the looks.

That's a good idea, but to tell you the complete truth I don't like illuminated buttons that much. I really love the great work behind getting them on an empeg, but I prefer the way non-illuminated buttons look like since they let the display stand out at night. Just my humble idea, of course
Also, I have a Anoface (Newface) which I really like and I was thinking to use that, which is black and hopefully will look nice.

how is the situation about the original A3 stereo? I mean, isn't that really heavily integrated? I hope not, of course, but I only saw cars with nav system, so maybe there are differences?

Fortunately it is not heavily integrated. It is slightly larger than a standard DIN, but Audi provides some plastic components that will fill the holes on the sides od any standard DIN head unit (like the empeg).
Since I was planning to install my empeg, I got the bas stereo system. I am now wondering how good is the amp+speakers installed by Audi (I don't know how many amps, 6 speakers, no sub). If it's decent, which I expect in such a high quality car, I may keep those at least initially to save some money...