Remove include_background_atoms setter

There's too much which relies on knowing whether we include backgrounds during initialization. We sort the primitive according to it, and then we have the ValidConcentrationFilter and so forth. I propose removing the setter for include_background_atoms, and only allow it in the constructor. And then set the value as soon as possible, so everything else knows whether the settings has background or not, and then we can always rely on that value being static.

Thoughts @davidkleiven @jinchang