Hi Peter,
I’m glad I’m not the only one with this issue. This has been driving me nuts.
I’ve been bugging Apple via their developer bug reporting tool about this since November 2012. I’ve posted a description of the problem here https://discussions.apple.com/message/20203301#20203301 and here https://www.fcp.co/forum/4-final-cut-pro-x-fcpx/15801-major-bug-audio-levels-incorrect-on-export.
Unfortunately as of FCP 10.0.9 it’s the same issue and it has been like this since 10.0.0. No response from Apple (Maybe I’m “holding” my mouse the wrong way?)
I’m surprised they can’t get it right since this has never been a problem in FCP 7.
And like you I don’t need to export stems for further editing. What I need is FCP X to output a finalized deliverable package combining my conformed audio tracks from Protools and the video.