Even if that WAS the case though ,that would ALSO mean that believing we have free will and are responsible for the consequences of our actions is _also_ a result of such programming… as would be believing we have no choice in the matter would be a result of such programming.
So, it makes trying to figure out “which is which” kind of a moot point.
Instead, we’d have to go up a layer of abstraction, since there’s no way for being within the system to see outside of the system, as you say.
Issues of pragmatics come into play then. What’s the better choice? (or non-choice, since there’s no way for us to know which is the truth from within it and there’s no way for us to get outside of it. Even if an alien species told us everything humanity is seeing wrong, we still couldn’t really see it from an objective perspecive because we’d STILL be within that system ourselves).