I believe the reason they don't show the bosses is probably because 1) it's a spoiler or 2) and this is my personal
belief but they're dead, I'm 90% convinced this plot takes place after the main game. for example, here's a snippet of chapter 8,
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Humans in the Deep City, tons of them almost touristy even, in fact the group talk to more humans in the deep city than they do in Armoroad with a severe lack of Yggs.
I'm sure the mangaka is trying to not touch on the main game's story for reasons (called atlus), since even the Untold group did their own thing after the introductions to each other and the main plot with MIKE