Sure, but throw it in a README.md, not in the code itself.
Besides, if you foster a culture of writing "why" docs, the problem of where to place these docs is one you solved early on, so people will know where to go.
Absolutely. If you were to survey, I would fall much more closely on the "don't comment code" side of things. But if you have documentation for your project, keep it close to the project. That's all.
Besides, if you foster a culture of writing "why" docs, the problem of where to place these docs is one you solved early on, so people will know where to go.