Because Payton is busy coaching the football team and they needed Ireland to run the scouting department. Just because a you have people that work for you handling the details doesn't mean you aren't in charge.
Maybe Payton didn't have total control. I think he did based on the evidence, but even if I'm wrong and he didn't, he clearly had a lot of power to do what he wanted with the roster and with the draft.
And, I'm not really blaming Payton for the current situation. DA, Ireland, and Loomis have had 3 years to fix it and they haven't. So all three of them share the blame for the current situation. But Payton did leave this team in a bad situation so I am blaming him for the situation that existed when he left. But Loomis, Ireland, and DA have done a bad job of making that situation better.