Two hierarchies, one for programmers, one for managers, with the managerial one viewed as above the programmers' one.

What does "above" mean? Managers necessarily tell the programmers what to do a lot of the time; that's just part of managing people. For humans, this seems to be inescapably tied to higher social status.

Is there a separate sense of "above" you refer to? Higher paychecks for managers are common. But then I might as well ask the more general question of why different job-tracks have different paychecks at similar levels of experience, seniority, and skill percentile. There are various reasons; one is that the top-level executives deciding on paycheck policy are usually promoted from the top ranks of the management track, rather than a technical one.