When you choose "Save and restore Window geometry for each document" and open a new document either
a) the default window size setting is used upon startup
and the window is positioned however GTK+ prefers
b) the window position/size from the default template is used,
obviously only if it is set in the default template
(not the case for the templates that ships with Inkscape)
When you choose "Save and restore Window geometry for each document" and open a new document either
a) the default window size setting is used upon startup
and the window is positioned however GTK+ prefers
b) the window position/size from the default template is used,
obviously only if it is set in the default template
(not the case for the templates that ships with Inkscape)