goes in = is stored in (ie, that's where bread "goes" when we put the bread there...because that's where bread is kept or stored)

Yep, u right

Yes. It tells you where to put the bread, meaning the bread is stored in the bread box that is behind the toaster.

"Goes in" means 'is stored in' or 'is kept in'. But we would usually say "bread goes in the bread bin" in a situation where we are telling somebody where to put it. We are telling them that the bread needs to travel from their hands to the bread bin.

It belongs in the breadbox. That's where it's normally kept.