I also perceived that those keyboards are played along (probably at the same track) with the main drum beat. You can notice that better at the end of the song, where the beat goes in and out, and the keyboards follow it, going in and out at the exactly same time.
i wish aphex twin would relase some more of his ambient stuff like this. he says he has albums worth of unreleased material, that he doesn't release simply because he thinks it is too original and too good and someone will copy it.... what i wouldn't give to get my hands on those tracks. i would say this track chills me out, but that would be a complete understatement. it takes me to another level, transforms me and my thoughts and brings me peace and acceptance... even if that sounds pretentious that's just how i feel about the track <3