> my window layout, among other things, is being saved by default to the Inkscape SVG file

There is a new setting (coming in 0.49) - "Save and restore documents viewport" - when unchecked - prevents the zoom and panning settings from being saved to the SVG. Hope this will help somewhat with shared access files.

> I couldn't get the "Windows -> Remember and use last window's geometry" option to work
This is now fixed (r11843) - window size and window location should not be written to the SVG anymore with this preference.