Short answer is don't edit the stock DMs. JSON files do not stack like regular conf files. Once you choose to edit you are in the commitment of hand reviewing and updating DM JSON files for your "branch". This was a very unfortunate development choice in file behavior for the JSON DM files vs regular conf files.
Your options are maintain non stock versions, being sneaky and being more creative with your onboarding such as merging contextual information into fields like signature so they make it through the stock data model or just live with the stock DMs if you use them.
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