This rebuttal is very weak. It’s attacking straw men, not really addressing the original article at all.

For example, Motl objects to Ball’s The world we’re living in sure doesn’t feel quantum mechanical by quoting himself(!): some people keep on saying that it "looks like" there must be a classical mechanism beneath the quantum phenomena.

That’s a ludicrous misreading of the article. Ball isn’t claiming that nature is somehow secretly classical, he’s saying it is quantum but looks classical in everyday life. Ball is in fact making the same claim as Motl himself, if only Motl could see it.

Or for another example, Motl objects to Ball’s How do quantum probabilities coalesce into the sharp focus of the classical world? and insists that they do not in fact coalesce: Statements about big objects' properties may "look" certain because quantum mechanics may predict probabilities to be 99.9999% or higher [...] But quantum mechanics never allows the certainty to go to 100%

Again, Motl is in violent agreement with Ball! The whole thrust of the article is that wave function collapse is not a special process outside of known quantum mechanics, doesn’t depend on consciousness, and doesn’t require an observer. It’s a statistical process where the probability of seeing a singular, classical-like state will tend towards 1 as a system interacts with its environment and decoheres.

And there are plenty more such examples. It seems like Motl in fact agrees with the article, but objects to... the tone for some reason?

Or maybe he just thinks it’s trivial? If so, I don’t think that’s fair at all, as wave function collapse really is widely depicted as highly mysterious, in pop science circles at least.

The rebuttal takes a view which is close to my heart—but [Motl] puts it so viciously, dismisses without genuine inquiry or curiosity the intriguing claims of the article, and plays so much faster and looser with his ideas than the author he critiques—you can taste his contrition. Ball and [Motl] are probably both mistaken about what QD actually explains.

Edit: fixed names

Motl is often too agressive and not fair to the target of his critiques, but when it's about quantamagazine vs. Motl he's the safe bet. (I've not read neither in this case, though.)