I studied psychology after I studied math, and the most funny thing that happened to me after the second: I become less concerned about truths and more about people, about what they say and why they say it.
There are two examples in the article. The first one is about nurses and masks, when author's girlfriend evidently tried to convey her compassion to nurses who need to wear masks all the day long, but the author didn't pick this message, he stumbled over untruth and was unable to just let it be. The second example is about his father, who probably tried to ask for help nicely, to ask in a way that doesn't feel obligatory to conform. But unfortunately the author saw an untruth in a message and was unable to resist an urge to start a holy war against falsehoods, so he missed an opportunity to help without realizing it.
The second example is illuminating: he missed an opportunity. Maybe he was not interested in it, in this case he lost nothing. But maybe he was interested (or rather would be interested if he picked it from conversation), and in this case his loss was very real. It is not about niceness per se, it is about seeing world around you as it is. You can be nice then, or to be not nice at all, but if you do not see where are opportunities to be nice, you are losing an opportunity to choose.
If being more analytical leads to the less understanding of the world around you, and therefore you are missing opportunities, than maybe an analytical approach is overrated?
Though I feel very empathic to STEM majors who was trained to fight a holy war against untruths and cannot resist it even when this holy war sidetracks them from the core of a conversation. It is not easy to overcome this training and moreover it may be not just training, but a natural disposition too: maybe people who are less concerned about people are attracted to (or pushed into) STEM carrier paths. I do not see their behavior as toxic, one just needs to clarify his/her message when STEM major stumbled over an untruth. It is just like talking with kids, they also tend to react to a wrong part of a message.