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To make things clearer for the OP:
Calibre does not interface or interact with ANY viewer other than it's own. When you disable this interaction in prefs, calibre will pass the "open this file" request to the OS after which it is up to the OS to deal with. Calibre it totally out of the picture at that point and knows nothing about what happens to the file. When you configure your OS to use some specific app to handle such "open this file" requests it will then pass the responsibility on to that app.
Doing things like remembering the last page read, etc., are the responsibility of the viewer, not calibre's library management. If your CBZ or PDF viewer opens the file at page one on a second viewing then it is at fault for not remembering the previous session. If this bothers you then use a different viewer.
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