Why would anyone choose the map rather than the territory as their foundation?

I couldn't agree more, which is why I was attempting to discourage people from doing so.

Why engage in science if you are not willing to accept the inferences that it makes about reality? Am I not going to believe in atoms because it doesn't match what I see with my eyes?

But the justification for any physical theory is precisely that it predicts what you see with your own eyes. Indeed, that's what a physical theory is - a means of predicting what you will experience. Atoms, as a feature of such a theory, seem quite useful and worth "believing" in.

Do you have any explanations of illusions?

Illusions are when your theory of what you should experience breaks down, and produces wrong answers.

when science makes steady progress it usually ends up with an explanation in materialistic terms.

But as I pointed out above, physics is not materialist, so your claim is untrue.