To set default magnification and scrolling options for a PDF file, go to File -> Properties -> Initial View, and set it up the way you like it (for a given file). E.g.:
If there are Bookmarks in the file, the layout changes when you click on one of them, relative to the Initial View. To enforce the same view, select a Bookmark, right click to get Properties, then select Edit under Actions, and change zoom to "Inherit Zoom". Unfortunately there is no built-in way to batch-set all bookmarks to this (unless you want to install something user-written).
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