Much can be done with those doors. (m)
A lot of what you can get done really depends on the skill level of the installer. My roomate has a 2001 A4 and he has Diamond Audio Hex 6.5's in the factory door locations. They were fit into the factory spot with no mods to the exterior of the door whatsoever. All the installer had to do was cut a beveled piece of wood to angle the speaker properly. It sounds great. I know many people have placed 5 1/4 speaks in the factory locations as well. If you're really serious about sound, you can go the route that others (including myself) have gone and put fiberglass kickpods in the footwells. I have Diamond Audio Hex 4" speakers and silk dome tweeters in the factory door locations, and a Diamond Audio Hex 5 1/4" speaker in a custom footwell kickpod. This summer I'll be swapping the 4" in the doors for a 6.5" DA Hex.
So to answer your question, yes, it IS possible to stuff a 6.5" driver in the door without modifying the door itself. It just depends on the particular speaker and the installer. DA Hex 6.5" are the only ones I've seen put into the door, so far, FWIW. Best of luck!
B