Whiffling Clara was also abandoned and returned to atmospheric induction. The pulsating inlet on a single is just too irregular. The more cylinders, the less this effect. I think it is significant that the only successful single cylinder supercharged bikes are Mighty Mouse and Super Mouse* - the issues of varying throttle disappear on a sprint bike.
In the 1980s, Honda turbocharged the CX650, and that had lots of problems due to the irregular and infrequent intake pulses.
* Super Mouse is a twin, but each cylinder has its own supercharger, so it functions as two singles.
Paul