I have this problem, that my workspace layout has pallettes docked to the right screenside. With multiple document windows set to non tabbed (see screenshot; red area), the initial opened window will extend under my pallettes (green area), making it impossible to see the scroll bar. Also the document page isnt centered (blue area), and objects on the pasteboard are dissapearing out of sight under my palettes (yellow area).

I have this covered by a start-up script with an event-listener 'afterOpen': app.layoutWindows[0].bounds = [81, 40, 1357, 1762];

But i'd like to see this as an option. Maybe in the document preferences.
Quark had this by default, but that wasn a good idea, because document windows got completly out of sight, if you open a Quark-doc on a machine with different double-monitor layout.