"Back when the open-source drivers relied on user-space mode-setting, affected users could use a variety of options within the xorg.conf to override values and handle quirks within the server. However, with kernel mode-setting that support is out the window."
You can still use custom configurations in your xorg.conf. That hasn't changed.
Do you think GNOME should be responsible for it? I can accept that the configuration you want for GNOME may not be the configuration you want for something else but it would be nice to have some common interface for handling this.
There is a common interface, and GNOME's display properties applet recently grew a button which applies the current GNOME configuration as the system-wide default.