Yes, the beat in Ghosts is formostly made of it's own stomping sounds. That's what you hear loud in the front. But underneath there is the BeeGees loop, layered below in lower volume.
The percussion sound (the mechanical sounding stuff between the single stomps) is the big giveaway. It's the same as in the BeeGees beat. It's played the same way and it has a very distinctive unique sound (sound design) to it, which is probably why Michael liked it.
And if you listen close you can also still hear the BeeGees cymbal (or 'sleight bell'?) in the Ghosts beat. (That high frequent regular simple rhythmic percussion sound.) The rest of the BeeGees beat is covered under the loud stomping beat of Ghosts.
I've chopped segments up and made a little demo to directly compare here:
https://soundcloud.com/verkauf/4x-ghosts-beegees
That's 1 bar Ghosts followed by 1 bar BeeGees (repeated 4 times).
I sped up the BeeGees loop a slight bit (2 bpm) so the tempi fit together.
Listen close over headphones to the percussion and the cymbal.