I would like to suggest a different or more nuanced reading of the advice. Namely, the advice is to avoid comments that only contain this.
I agree it can be appropriate and nice if a questioner thanks the other (or all people) that provided answers beyond an accept and an upvote. Or, also other communication in the comments.
However, I also think that it can be still nicer if the comment is not only a quick "Thanks!" (plus something to get over the character limit) but actucallyactually says something specific or personal, for instance in the situation described it is not unlikely one could highlight a point that one specifically appreciated about this one answer.
Or, put differently, a 'thanks' comment can be appropriate but I think in most cases a comment containing not only 'thanks' but also something in addition can be even more appropriate.
Still put differently and somewhat jokingly, if somebody often writes comments containing only 'thanks' they do not put enough effort into expressing their gratidudegratitude.
I should also add that it is my understanding that this reading of the advice is not an absurd one (relative to its intent). Also comments should add some information, a comment that thanks in a specific and somewhat detailed way does, only "thanks" does not.