Simes,I too have transmission clunk and have been told it is the way I drive.I have never owned any thing other than a manual car and have only experienced this "clunk" or "thud" on gearchange on worn out cars not new ones.I also have never worn out a clutch in my life. I drove a brand new Brera 3.2 and it also "clunked".Alfa have a problem and don't want to admit it.Why are they so careless?Surely they would have experienced it during testing.The fact they all do it as they said to you and me is not the point,the fact is they have screwed up.It is an unbearable fault and is unacceptable.Good on you for pursuing it and I will do the same here in Australia.
After mutch faffing with mine and yes alfa told me it's the way I drive - I just threw the dealer principal the keys and made him drive it - it was the way he drove it too - we then spent three months finding the fault with Trofeo (alfa uk technical) involving replacement of all the oil (with no supplies in the UK), diff's, gearbox, a propshaft we managed to persuade alfa to authorise removal of the clutch assembly - lo and behold the dual mass flywheel has about 4-5 times the amount of slip that was normal - so was managing to slip beyond the cushioning and thereby create the thuds - two or three 3.2's to my knowledge have had the fault.
To cut a long story short after 14months I gave up on the brera - couldn't be arsed with a replacement - numbers of the early owners did - I didn't so took it on the chin and left Alfa until they can get their act together. It was a fairly painful experience in the wallet department but as I know my way around the dealers better than most of the staff I had also done over 5K miles in their cars this year - something had to give.
I now have 2 cars - a nice new porsche cayman that's everything the brera could have been and wasn't - handling, acceleration, controllability and pin perfect with over 32mpg economy on a run for 4K more than the brera cost new. and a Panda 100HP likewise but over 47mpg on a run - as I said to the supplyign dealer - same dealer I sold the brera to - if the alfa had been this good - we wouldn't be where we are.
I still love alfa's the brera was my 5th but after 14months in a brera that was **never** right from day 1 and with sod all support from ARUK I'd just had enough Mangoletsi had tried their best but the car was not right and was never going to be right - and I had little hope of a replacement being better.
Hope you get yours sorted - and enjoy her before you end up like me...