Interesting test. However, I'd like to mention a few points as it's a forum:
I don't see how you could compare the two engines (i know you mentioned price) but ignoring the old petrol vs diesel debate - the 2.0 TDi isn't exactly a sporty example (you didn't mention if it was the 170 model, so i'm assuming it's the 140)
With regards to the torque, I know you mentioned in-gear acceleration but I think you're getting that mixed up with torque - the Type-R's v-tec and higher rev range more than makes up for having almost 100 lbft torque less but it isn't exactly torquey.
I'm also amazed at the ride quality (I know you said you were surprised too) but i've been in a 2.0TDi with 18" wheels and it still felt less crashy than my CTDi with 16" wheels.
And to prove i'm not against the Civic and for the Audi - I absolutely love the audio/ventilation set-up of the Civic, it's close to hand, up near eye-level and quick and easy to use. The A3 ventilation in particular is set a lot lower down and often requires taking your eye of the road for that little bit longer as you look down, especially if it's fitted with climate control rather than just manual air-con.
Please don't think i'm getting at you, just adding my two-bobs worth. I love comparison tests. Especially as they are more accurate than the ones you see in the likes of What Car or Auto Express.