I would think that we can both be accommodated - if "mark as read after n seconds" is selected with n = 0.0 you would get your insta-marked-as-read behaviour; for me, I would have that option unselected, and there should be no automatic marking as read regardless of whether I see a message in a preview pane or in a separate message window.
This is how I wanted it to work in 2.0 and it did for a while, but I got rolled by higher up, to cater for people who couldn't be bothered to actually read what the checkbox said.
So i'm going to be a grumpy bum and leave it to others to 'fix', since I had a go but my go got thrown away.
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