and except for possible thermal issues with the bond totally the same electrically... I do hope they have the bonding right...
Hmm, you bring up an interesting question about thermal issues Doc. Copper is more thermally conductive than gold, 401 W/(m·K) vs. 318 W/(m·K). This by itself would be a potentially good thing, meaning heat can flow out of the die a little faster. However, the rate of thermal expansion is also slightly higher, 16.5 µm/(m·K) vs. 14.2 µm/(m·K) (both @ 25 °C). Expansion and contraction due to heating and cooling will put mechanical stress and strain on the joints, and it will be proportional to the rate of thermal expansion. Still I don't know if the higher thermal expansion will matter enough to be a problem, even at the small scale of die-to-package wire bounding. On the other hand, I don't know enough to rule it out either.
After scanning through both Sections 29 and 30 (Section 30 has the typical characteristics for the different part numbers), I haven't noticed any significant changes. Since the datasheets don't seem to have changed, we'll just have 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.