Screenshots would be helpful, because (you may be surprised to learn that) it is not entirely obvious which mode of behavior is supposed to be "wrong".

Anyway, I wouldn't say it currently behaves nicely (like something I would like to reuse anywhere whatsoever). Tested on Firefox opening Bookmarks on the left. First off, there is this ugly flicker, as browser first renders the "wrong" version, then your JS "fixes" it. Second, there is some concurrency problem, as by opening and closing Bookmarks repeatedly I somehow managed to render both versions: centered to viewport and covered by sidebar.

And, yeah, as others have said, I also think that allowing sidebar to cover your webpage content is absolutely bogus and don't foresee myself wanting this behavior, ever. But that's up to you.