and except for possible thermal issues with the bond totally the same electrically... I do hope they have the bonding right...Doc
It would be nieve to think that someone at ATmel (or virtually another company dealing with parts rooted in metallurgy) didn't consider the CTE differences between Al and Au.
hope that before making this change to their manufacturing process Atmel did adequate testing to ensure this new bonding technique wouldn't have an appreciably negative effect on their ICs' reliability or performance.
I would rather think that Atmel is 'running' on the evident success of others, time will tell though.