I have the same experience when generating a plist file for a self-developed agent.
Some background to the situation: The plist was written directly to the ~/Library/LaunchAgents folder using the python plistlib and standard python file creation: open(fileName) as fp:. The result was a correctly formatted plist file but with the com.apple.provenance attribute added. launchctl gives errors trying to load or bootstrap the file.
As in the OP's case xattr -d simply does not work on this extended attribute.
For the next attempt I'll try generating the file in a different folder then copying it to the ~/Library/LaunchAgents folder. I'll post an update in a couple of days.
bldrvnlw
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