The short answer is that neither would be ideal. The 03-08 version is pre-facelift, and so there will be differences all over the car (engine and body); they'll be slight for the most part, so it might be useful as a guide, but there will be stuff that's not exactly right. Similarly with the one for 09-12, the body stuff will be OK, but of course your engine and anything tied to the engine type won't be right.
I don't know if there's a Bentley manual for A3 8P, it might be worth a look. Audi use a system called ELSAWin for electronic manuals (which isn't supposed to be available to end users and generally requires you to be pretty handy with computers to run).
R