The RT_SiteConfig.pm file is to preserve your settings between upgrades.
You should never make any changes to RT_Config.pm - that is what RT_SiteConfig.pm is for. So for any changes you want made, copy the variables from RT_Config.pm and set them to your spec's in RT_SiteConfig.pm..
NOTE: This does not use the logic of the _local_-directory (see: CustomizingWithLocalDir) where the file is completely replaced. Here only the vars set in RT_SiteConfig.pm override those specific vars in RT_Config.pm, the rest of the vars in RT_Config.pm are left unchanged and still in action.