Just listened. I'd be more inclined that he is messing with us by making up that backstory than him actually messing with the airline. Or it's just some random piece of invented mythology that someone came up with and came to be accepted as true.

>check "aphex airlines"
>
>rumor:
>
>"Richard was commissioned by Virgin Airlines to write a song
>for a television commercial, and he came up with the track
>Aphex Airlines. According to him, the song is supposed to
>represent how a jet engine feels at take off. Not
>surprisingly, the Virgin people didn't feel that the song
>would be very appropriate, they thought it would make people
>think of airplane crashes."
>
>in fact, this appears on a compilation released by virgin
>records, so the rest might be embellishment