A note explaining intent of local identifiers / lid may be helpful indeed. I created Explain intent of local identifiers in a note in the spec · Issue #1740 · json-api/json-api · GitHub to track it.
The assumption was that many extensions need local identifiers. It was added to base specification to avoid multiple solutions to the same problem and compatibility issues. If I got it right. @dgeb feel free to correct me as I wasn’t part of the discussions at that time.