I’m sorry, but your are wrong. I’m a programmer myself, I actually do that for a living, and I’ve come across this very same problem. We had an application where users had to click a checkbox to activate manual override, and in a second step had to choose or enter their own value. They didn’t like it from the very beginning and we had to change it.
It could be as simple as 3-state-elements (checked / not checked / “not set”) that you see in every application installer.
All I’m saying is: There are ways, if you really want the user experience to be more fluent in this area.