I and most other people are riding around on stock engines with stock exhausts. Those confirm to stricter quiet standards in Japan than anywhere in the US.
To your second point, modern car engines have efficiency gains due to important innovations like direct fuel injection, whereas most motorcycles are stuck with port injection, a limitation currently forced by the fear of having a very high pressure fuel pump between rider’s legs…
In spite of that, total bike emissions are lower for the same distance vs a car, we’re not lugging an entire chassis, air conditioning etc. The result is that even carbureted bikes from the 80s could go 55-60mpg. Bikes also have much lower engine displacement, your v6 2L has about 2000 cm^3 of air and fuel burned per revolution, whereas most motorcycles are in the 6-800 cm^3 range, per rev.
Manufacturers could make them quieter, but that adds both weight and cost, more of one if you adjust the other. I look forward to electric bikes with great range, as I don’t really do more than 350 miles on my long trips unless I’m late for something.
E: looks like Japan relaxed their standards since 2013, per some internal documentation, see slide 9 for harmonized requirements. Still quiet, all things considered.