That's because software architects are wrapped up with building architects on Indeed. Building architects make much less: https://www.glassdoor.com/Salaries/architect-salary-SRCH_KO0...
(Which is partially why I left.)
If you compared the salary of an in-n-out manager to the engineer running the team, or to law firm partners, you'd get a different conclusion.
The fact that someone who's worked for a good chunk of their life at an In-N-Out makes more than a young professional fresh out of school seems pretty reasonable, when you think about it. (Although it still makes In-N-Out an exception, which is too bad.)
With almost certainly far more hours worked to make that salary, as well. Most fast food managers are spending 60+ hours/week in the store, opening early and closing late at night. All to make a decent living wage in California. I would not envy that life one bit.