As for running MClean separately instead of as a prefilter, it considerably decrades the quality.
Prefilter / Denoise (both in 16-bit)
I'm getting best results with MClean(rn=10) in 16-bit, but am unable to use it as a prefilter in 16-bit and can't figure out why. Additionally, I'm unable to get a decent encoding done with FRC Preset=slower combined with MClean. But ultimately, that would give the best.