Nice little detail of Mike using soft beaters on his drums in the first half of the song.
I don't know about soft beats, but I do remember it being the only time that one of his extra kick drums really ended up having a use. Most of the time they generally sound the same, even if he claims he's using them for different things, they sound the same. In this song, it sounded like a very different kick drum, and that was a great choice.
Based on the live performance, he's not hitting a kick drum.
https://www.youtube.com/watch?v=xNgD02iTcNU
Fascinating! In that case, it's a really cool use of a drum that even Portnoy I believe had but never really used in a unique way. Either way, bravo for using a drum in a new way for Dream Theater.