There is no way the clipping bug is gone. Try playing the song w/o Roon. Use the local library playback with relaygain turned off. Try the song "waste" by Rhye. I thing you have a Roon bug that adds some attenuation.
The change from hearing the crackling to not hearing it was with Roon only.
Agree It's certainly not a NAD bug fix as no new firmware has been loaded.
Also no new Roon update so it's not that either.
I did try the Rhye song and yep, clipping is there via Roon with no headroom adjustment.
As for the M33 overall, the clipping issue when using subs is of course something they should address but it makes a 10/10 product a 9/10, imo, not a 'mess'. I guess we all have our own tolerances for what is acceptable and not.
For me, as I can easily solve the issue with Roon DSP, it's just not that big a deal, but for those without a method to make the adjustment pre the M33 receiving the data, I can see why it is a bigger problem.