On the subject of premix. When you slam the throttle closed at the end of the chute you do indeed cut off the majority of the fueling, but you do still have the pilot jet in there to bleed fuel in. Blipping the throttle certainly helps, but if the fueling is correct and the cooling system efficient you shouldn't have any problems.
How many of the 125/250's seized at the GP last weekend? Maybe a couple over the duration of testing qualifying etc, but it certainly isn't a common problem these days.
As for jetting. Think of the motor as 2 125cc engines and jet each one according to it's requirements. Don't ever think that because #1 got this size jet, #2 must have it as well. If you're a couple of main jet sizes different it's not unusual (as Tom Jones would say).