Tokens in greetings not replaced
It sounds like the hook isn't being called (or not called correctly) when processing the update_greeting job. I think that qualifies as a bug and you could file it in issues.civicrm.org. But due to the high volume of issues, a core team member may not be available to jump on it anytime soon. I'd suggest you keep on with your debugging and compare the code that runs during that scheduled job to the code that correctly uses the hook and see how they differ. If you are able to come up with a patch that even partially addresses the problem it would help the issue get a lot more attention (issues with patches get bumped up in priority).