Not SEt's AviSynth MT, rather
pinterf's AviSynth+ MT (and I would be surprised if MeGUI does not update this once in a while).
It doesn't matter how many cores MeGUI uses, because MeGUI is only a user interface to build the AviSynth script. AviSynth+ has to use all cores when it executes the script. For AviSynth+, this requires a
Prefetch(number_of_cores) call at the end of the script. You may have to add it manually. And there will not be a guarantee for 100% CPU utilization ever. Also note that the encoder will need some CPU time too, and often more than the AviSynth filter chain.