When using desmume or desmume-glade, the $HOME/.config/file only contains [KEY] and [JOYSTICK] sections.
So the window size or the SPU mode setings will not saved and need to be set everytime.
Regarding windows size on X11 desktops AFAIK this is not something the application does, there are tools like these if your window manager does not have that feature, like http://burtonini.com/blog/computers/devilspie
Moving to feature requests.
Taking over this. See [bugs:#1351]
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