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Yes - iTunes uses Quicktime, and Quicktime has one of the better AAC encoders. Unfortunately, it's not easily executable (or licensable) on Linux.

Can you comment on which actual encoder you're now using, or do you consider that a secret?

Looks like a secret: http://news.ycombinator.com/item?id=2787570 (a comment elsewhere on this page).

Yep, unfortunately we can't right now. Maybe down the road?