This is uncharitable to the point of seeming like a deliberate misread.

The bathroom anecdote is just a memorable illustration of Carmack's mindset: only work counts as work. Neither Carmack nor the author thinks you should avoid the bathroom or feel bad about pissing.

This is a self-aware blog post of a guy who worked with John Carmack and was able to use that to honestly assess his own productivity, and the amount of time he wasn't focused.