So, if the single pilot a/c certificated for operation by just one pilot, has two pilots then, by implication, it shouldn't/can't fly.
Yessir. And by extension, licensed pilots (regardless of licenses/ratings held) cannot fly as passengers on commercial aircraft. As these are typically two-pilot aircraft, any extra pilot on board would be cause for immediate grounding.
This is why commercial pilots don't wear uniforms or anything that makes them recognisable as pilots, when they're on board a commercial airliner as pax. It keeps them under the radar so the authorities don't know an illegal flight (3 pilots on board a 2-pilot aircraft) is taking place. And it's also the reason why flight crew don't appreciate private pilots identifying themselves to them before take-off: It leads to all sorts of unnecessary complications and paperwork. Best to stay quiet about it or you run the risk of being offloaded.