And these profits are then used to sustain the organization in the long-term, IE carried over for future operating costs. Per your own source,
it cannot be used for the benefit of any private party.
"The figures you see?" That sounds an awful lot like, "many people are saying." It's anecdotal at best, just an opinion formed out of preexisting biases at worst.
Again per your own source, 92 percent of all nonprofits take in revenue of less than one million a year. Logically then, no individual within one of those organizations can possibly be earning millions by themselves.
Correct, an individual cannot legally use a nonprofit's bank account as a slush fund, which is what the Trump Foundation got shut down for. And yes there are ways around that for smart criminals, but in general it's much easier to start a PAC/super PAC to conceal any sort of fraud/money laundering/tax evasion, as there's far less scrutiny into those.