I think you are talking about something different now. My point us that its not Pep's job to fit any player in. Its his job to put forth his believed best team to try to achieve the most success.
Now if the higher-ups think he isn't doing that, then their role is to fire him and find someone who they think will do the job better.
That aside, my point still stands, so long as he is manager, he is under no obligation to play any specific player.
As it relates to Gonzo specifically, while I like him personally, i don't think his lack of game time is some huge error. He has been the most dispossessed midfielder while playing the 6. Three different times. Some of those leading to goals or major chances. We are kidding ourselves thinking Pep isn't aware of this.
He fixed the error at 6 with a double pivot ( primarily Kova/Bernardo). So while i feel for Gonzo, there are more than enough legit explanations for why Pep didn't play him.