No, I thought that by saying 'not-stupid' you were saying that your original example of 'everything is made up of atoms' had in fact been chosen fairly casually as a quick example to serve your own purposes, and that whilst you acknowledge that there are indeed things that are not made up of atoms you wished the logic of the example to stand by means of you and I politely agreeing to ignore all the things that are not made up of atoms in our mutual definition of 'everything'. So by 'not-stupid' I assumed you meant something approximating to 'not-nitpicking'.

So yes, I was misunderstanding how you use the term 'not-stupid'.