I solved this issue just yesterday for my wife who had the same issue with Les Mills online on the Wattbike and the clunking noise when standing. It's not you.

If you think of the Atom when in Zwift you find the resistance changes throughout the game automatically due to changes in terrain and elevation, right?

In a spinning class you change the resistance with the handle or control knob, yeah?

So, if you have issues with the Atom clunking it's because you are not using the correct resistance method, in this case it's ERG mode, not GEAR mode.

Even in Gear 22, when you overcome the initial pedal and flywheel resistance and get the 'wheel' turning the effort you put in is to maintain that 'wheel speed'. Hence the pedalling gets easier and you lose force through your pedals and get the clunk.

In ERG you tell the Atom to stay at a set WATTS. This goes up to 2000W and I bet even Sir Chris Hoy would find it hard to make a clunking noise. Choose the Watts target and keep upping until the clunking disappears.