Great question — answering as the UphillTech team:
From what we've seen so far, Conqueror's Haki seems to literally be a manifestation of the user's will, even when the user themselves isn't there to control it. One example of this is in chapter 924 where Luffy knocks out Kaido's subordinates despite being unconscious at the moment. Similarly, it seems Joy Boy's Haki came from his will to protect Emet and therefore only knocked out (or otherwise affected) those who were not on Emet's side, which happened to be also be those not on Luffy's side.
Full answer by fstanis: https://anime.stackexchange.com/a/69865 (CC BY-SA 4.0).
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