I honestly think it’s just patience and a true enjoyment of the meticulous nature of it, with a healthy dose of intuition for rhythm
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I always heard him, and Squarepusher, as totally deliberate. Their drum patterns have a melody and journey to them.
I spent a lot of time listening to (and trying to copy) jungle over the transition phase between hardcore and d&b, which is also deliberate. I think I read Omni Trio in an interview from the time talking about “drum song”… So Aphex’ and Squarepusher sounded like an extreme version of that. I found the generative stuff, and even the random/crossfader stuff you can do with OctaTrack very odd after such “schooling” in the deliberate method.
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For sure. I love how Squarepusher’s use of the amen break in particular often pitches the snare up and down, not sure if he’s going for a specific melody but it does sound melodic for sure.
One thing that I took a little too long to notice is that a lot of the more detailed drum composers out there, especially Aphex, often use a consistent snare on the 2 and 4 as an anchor while the other drums go wild around them. There’s definitely more to it, like having an ear for syncopation, treating it more like jazz drumming etc, but it’s surprising how even the most chaotic/random drum programming can sound focused and clean with a consistent snare. That single method alone took my drum programming from incoherent and amateurish to sounding like I kinda knew what I was doing 
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This book seems to be available under different titles on various mediums, but well worth the price and time IMO
SongBeats: Finite to Infinity W.E. Powelson
Time Signatures: Finite to Infinity W.E. Powelson