Removing sections from ini

Is there anyway to prevent a section from being included within the ini files? For instance, BaseEngine.ini includes references to /Script/OnlineSubsystemUtils.OnlineBeaconHost. I have disabled the OnlineSubsystemPlugins since we are not suing them and want to remove the references in the ini files. I hate to edit BaseEngine.ini directly since we may have other games/products in the future that require these features. I just want to exclude them in DefaultEngine.ini if possible. I tried -[/Script/OnlineSubsystemUtils.OnlineBeaconHost] like you can do to the key/value pairs, but it results in errors. I suspect that the only path forward is to edit BaseEngine.ini directly?