Pretty sure this is the exception to their principle. I've always heard this song like you describe, with the intro, the verse, the breakdown and the last hit of the song landing on the one - with the cymbal crashes denoting the downbeat of every new phrase. And then you have the hi hats counting "cheekily" and the breakdown snares being syncopated.
I aligned the two interpretations of the meter with a metronome, and the hi hats is the only thing that makes sense in the first version. Even with the metronome screaming ONE for every bar, you can't really hear it musically.
In other noted examples - like Spirits in the Material World and Battery - there are parts in the song where the one becomes indisputable, and the meter can be extrapolated from there to the rest of the song. Combustion doesn't have this. 🙂
Also... Tool-iest riff in the Meshuggah catalogue?