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.
And it sounds like you and I have no disagreement over what the point was, so where is the dishonest misreading? The phrasing of "fucking" around came from the author. Notice that the top posts on this discussion thread all have the same response. We all read the same point.
To repeat myself, going to the bathroom is productivity. Similarly, not paying for healthcare is externalization and it is not increasing the net productivity of the individual just because a hypothetical Amazon gets to pocket the difference. This bathroom anecdote just happens to be what Amazon thinks of warehouse productivity.
This guy is talking about being productive as an individual, he is not talking about how you can play accounting with your body and apportion productivity wins to Amazon while externalizing the penalties to yourself.
Early in my career I had an issue of not getting things done. I later learned about myself that I just have some needs to make sure my values are aligned to the work which required a pivot to another company. But everyone has their own reasons for not being “better”!
Breaks are necessary, and paid time, certainly - I'm not masochist enough to deduct every small break from my work time - but neither is John Carmack, nor is the author arguing for that.
This is just a blog post of a guy fawning over John Carmack and dealing with feelings of not measuring up.