true .. stock compression ratio is higher on the slower bike. High compression improves low-end torque and since the bike (in stock trim) is never gonna reach high speed there's no danger of high compression ratio causing cylinder-head heat problems.
Butterfly carbs are a lot different than slide carbs. There is no slide to adjust venturi size and no jet needle to meter part-throttle fuel delivery. The butterfly carb's part-throttle metering completely depends on the (what would be the "needle") jet size in the center of the venturi and on the air bleed circuit and emuslification tube under it.
One good thing about the butterfly carb is that it can, size for size and all other things being equal, pass a lot more air and fuel than can a slide carb.
A slide carb has a slide that travels up and down in a wide groove cut into the walls of the throat. The sides of the groove often have sharp corners which causes turbulence. The slide itself obstructs air flow. So, air flow past and under the slide causes lots of air resistance.
But a butterfly carb has a smooth, unobstructed throat from one end to the other and flows much better. (This superior flow along with the huge #78 jet is probably the reason that, in my experience, adding a performance exhaust and gaining over a thousand RPM didn't require a change in main jets.)
My guess as to why the slower bike would have a larger mainjet is that it's carb is tuned strictly for lower speeds. A richer mixture is needed at lower speeds since air flow is slower and fuel atomization is poor. Larger drops of fuel don't burn. If fuel doesn't burn it may as well not even be there. And when fuel "isn't there" the mixture that does burn is burning lean. A larger mainjet probably helps correct this condition.