Personally, I believe the commutating amplifiers were simply not reliable enough in the long term and had difficulty into low impedance loads. They also used extra componentry and more complicated PSUs along with at least another pair of filter caps- all cost money. Pretty much every commutating amp I have worked on (everything from the protons, to NADs(powertracker/PE), Kenwood basics, Pioneer A80/90s, Marantz AVSS etc) were only slightly spectacular when they worked and that wasn't ever for long. Low impedance speakers became the norm and most of these amps had to be forced to run the LV rails for 4 ohm speakers. If you were brave, you'd run the 8ohm setting (the HV rails) on 4/6ohm speakers and run the risk of the thing blowing up. The switching circuits were also prone to introduce spikes in the waveforms when toggling between the LV and HV rails.
The proton was one of the earliest and arguably the best of any I ever heard/owned. The 100w rating is FTC and even that was conservative, but throw a 4 ohm reactive load on it and you could be picking up the pieces. It was fun to see 400+watt peaks from it though!
I would bet most of the commutating rail amps of the 1980s are in landfill now.