It's not just an issue with intuition it simply makes it far harder to do many types of layout. One of the biggest failings of the W3C model was that you could

It's not just an issue with intuition it simply makes it far harder to do many types of layout. One of the biggest failings of the W3C model was that you could not combine a percentage width with fixed margin. If you wanted a fluid layout but which still incorporated consistent margins it was impossible to achieve without an entirely unnecessary nesting of divs. Border-box completely eliminated this and poor old Microsoft (in this one instance) were forced to fall in with the less helpful "standard".