I think you need to register a GUI factory for you mod. See line 408 of net.minecraftforge.fml.client.gui.GuiModList. Unfortunately, I'm not quite sure how you do that. I would suspect it has to do with ScreenManager, like Block GUIs do.
Ok, my config toml file is getting populated with values, but the config button on the main menu's mods list is still grayed out.
(And yes, the description there is wrong, I put the wrong one in the toml file)