The man doth protest too much, methinks
An NFL organization is not a military unit and many many organizations have dotted line reporting structures where multiple people and offices report to multiple different people. That is the way modern organizations are run.
Only the most high level of decisions would need to go vertically to the top. Such as who is going to be the HC. Do you think they are going to give a first time HC the power to trade a first round draft pick for Tony Romo? No. Do you think Whaley cares who is the third TE or back-up interior lineman. No. Do you think they need to compromise and work with each other when making 53 man roster decisions in terms of the draft, the salary cap, and the make-up of the team. Yes. This is not so difficult.
The media is making it sound dysfunctional because they have an agenda against Whaley and Pegula.
So if Whaley is gone if they do poorly next year why would he get rid of TT with no other option? It makes no sense. Whaley said they were close. He said Rex's defense wasn't good enough. He just hired the guy to fix the defense. Pegs knew Whaley wasn't fully on board with Rex and Pegs knows he messed up with that hire. This time he gave Whaley full control. You are correct that he is on thin ice. If the new HC doesn't fix the defense or if whatever they do at QB/OC is worse than this year then Whaley is probably gone too. But then you end up in the 49ers situation with a new GM with a HC from an old GM. My hunch is Whaley is safe if McDermott looks like a capable guy.