And how are people supposed to make the distinction between your fun and signs of pathological narcissism?

I don't see this as a particular problem in this instance. The responses are of the form that if anything an indication that he isn't taking himself too seriously. The more pathologically narcissistic type tend to be more somber about their power and image.

No, if there was a problem here it would be if the joke was in poor taste. In particular if there were those that had been given the impression that Eliezer's power or Narcissism really was corrupting his thinking. If he had begun to use his power arbitrarily on his own whim or if his arrogance had left him incapable of receiving feedback or perceiving the consequences his actions have on others or even himself. Basically, jokes about how arrogant and narcissistic one is only work when people don't perceive you as actually having problems in that regard. If you really do have real arrogance problems then joking that you have them while completely not acknowledging the problem makes you look grossly out of touch and socially awkward.

For my part, however, I don't have any direct problem with Eliezer appreciating this kind of reasoning. It does strike me as a tad naive of him and I do agree that it is the kind of thing that makes Luke's job harder. Just... as far as PR missteps made by Eliezer this seems so utterly trivial as to be barely worth mentioning.

How do I make the distinction between a guy who has an "arrogance problem" and has fun encouraging comments that imply that people think of him as a god vs. a guy with a serious issue?

The way I make such distinctions is to basically ignore 'superficial arrogance'. I look at the real symptoms. The ones that matter and have potential direct consequences. I look at their ability to comprehend the words of others---particularly those others without the power to 'force' them to update. I look at how much care they take in exercising whatever power they do have. I look at how confident they are in their beliefs and compare that to how often those beliefs are correct.