Idk, Payton said on numerous occasions how much respect he had for the Bensons and the organization. He also had a huge hand in what players they brought in, injury risk or not. The latter of which was partially in an effort to save money due to salary cap manipulation. I believe he had a part in that as well. Helped him get the toys he wanted.
I think Covid, officiating, Goodell and other factors within the NFL as a whole just made him want to do a hard reset.
The crime and overall state of the city didn't help.

I’d find it hard to believe that he’d win a SB with a team then have doubts about their leadership. Producing the offensive success he had with Brees put him on another level of coaching as well. You mention a couple coaches that stayed put but plenty of others like Reid and his main mentor Parcells had success at multiple organizations. It is not surprising that you’d find an angle that bashes Loomis and company.

Not to mention that the same Ownership and GM believed in Payton, when he strung together multiple lackluster seasons.

Regardless, Payton isn't our coach anymore so it really doesn't matter what he has to say or what people "think he's thinking" lol just move on.