Now that you mention the Mouri family, you reminded me of something: Wasn't Kogoro weirdly absent for a good part of the Clash of Red and Black? His absence even mentioned by Ran, but later (IIRC) left unaddressed?
Maybe I missed something, but it left quite a large question mark in my head.
Though I don't think this would be at all related to the boss (unless later on it was revealed that it was. That only if I'm right and it's an unresolved issue...).
But going back to "who's the boss", I don't think it'd be necessary to show a character with That Man's qualities around, as he might simply be hiding them or feigning ignorance/stupidity. So That Man could actually be someone who's always there, but we're led to think he's not.
Chekhov MacGuffin wrote:
I think being specific about the name of the boss appearing instead of just saying the simpler "boss has appeared" was an inadvertent hint that the boss hasn't appeared yet in person.
I dunno... Saying "the boss's name has appeared in the manga" is not saying "the boss hasn't appeared in the manga yet, only his name". By saying he put the name in the manga, he could be confirming that That Man is not a yet-unnamed character, while not having to confirm that he already got an appearance in the story.
And this is Aoyama-sensei we're talking about, the guy who likes to play with what's said and what's not, and what's seen and what's not, in order to create his murder cases. I would imagine he'd carefully pick what he says in interviews.