Let me restate this for clarity. If the SOURCE video has a XML and EDL file along with it, the XML file is used to get metadata about the file. The EDL file is copied into the working directory.
After the conversion, if Skip Cutting Ad's is checked, if MCEBuddy finds a EDL and XML file (which is generated using Comskip.ini) in the working directory it copies them both over the destination.
Your issue is that the XML file you have contains the commercial skipping data where as MCEBuddy uses it to extract metadata. So it's not possible what you're asking.
You only option is to not put an EDL / XML file, rather have Comskip analyze and generate one during the processing and them MCEBuddy will copy it over.
After the conversion, if Skip Cutting Ad's is checked, if MCEBuddy finds a EDL and XML file (which is generated using Comskip.ini) in the working directory it copies them both over the destination.
Your issue is that the XML file you have contains the commercial skipping data where as MCEBuddy uses it to extract metadata. So it's not possible what you're asking.
You only option is to not put an EDL / XML file, rather have Comskip analyze and generate one during the processing and them MCEBuddy will copy it over.