You must edit /etc/X11/xorg.conf to tell GDM what resolution to use or it will just guess. Yes, changing the resolution in your GNOME session only applies to your session.
For example at the bottom of the file, add in a Modes line like this:
SubSection "Display"
Viewport 0 0
Depth 24
Modes "1024x768"
EndSubSection
EndSection
The refresh rate is defined in the Monitor section of this file with HorizSync and VertRefresh.
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