Sounds like you've heard the remaster with the bonus studio version of Clap. They weren't really happy with it so went with the live version - makes sense, the studio version is bone dry.
The Yes Album is absolutely my favourite album of all time, and also one of my favourite bass albums, unsurprisingly. It's the sound of a band starting to realise their genius, but still full of youthful exuberance and holding on to their poppier beginnings - arguably they wouldn't hit their instrumental peak until Wakeman joined but here Tony Kaye's earthy, grinding Hammond really grounds the band and holds them back from some of the whimsy to come.
A truly joyous album, with Squire's short bass solo in Starship Trooper - climbing up to briefly peek through the clouds - one of the most glorious sounds I've ever heard.
I also think Clap absolutely fits and the album flows perfectly.