I did encounter the same problem of reformating documents and the reader still shows them as if I hadn't done anything.
For the zoom thingy, I actually like that zoom resets on page turns. If you try a magazine where articles are spread over a page randomly, the full page view gives you a pretty nice overview on where you want to zoom in.
Occasionally I found the zoom reset annoying too. That is when a document was formatted the same from page to page.
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