I realized the manual is not very clear about this but, as with many things in GSX, you can create your custom configurations to override stock files, without having to change them.
If you create a new rules_handling.cfg file in the %APPDATA%\Virtuali\GSX\texture folder, containing ONLY the sections for the operators you want to change, those operators defined there will be read from this file instead of the stock one, so you can keep the main stock rules updated, and your custom changes selected operators.
This works for all rules files, handling, catering and jetways.