It's actually really simple. JB isn't good at throwing the ball down the field, and he and the staff know it.
You keep presenting this argument that throwing downfield isn't valuable, and that's just dead wrong. But that's a discussion for another day.
You and others also keep presenting this argument that, because the receivers aren't the guys the team expected to have at the beginning of the year, it's not possible to be productive throwing down the field. But there's a reason players wear the same color uniform in games, and we have ocular proof of receivers open in various spots on the field, including down the field, but not being targeted. The first prerequisite for downfield production is receivers getting open; the second is the QB throwing the ball. The first is happening, the second is not.
We don't need to muddy the waters on this, even though that's your MO. It's clear cut, plain and obvious. JB has bad downfield numbers because he's not good at that part of the game.