The stocker pipes probably won't switch easily. Never tried.
On most after market stuff, the pipes are specific to the model, so no go there either. Not always the case though. Harc pipes for example are actually all MC28. They hit the swingarm on the MC1 right side, but it doesn't concern them, so why should it concern you?!
What exactly is your plan? If you've got a 28 but think that the stocker 21 pipes would work better then you're right to a point. they will give more power, but mainly only because the head pipe has a bigger inlet. 40mm on the 21 compared to 30mm on the 28 (silly restriction). If you want a simple 4 hp then get your rotary grinder out and whizz the ring out to 40mm. Easy job. Fit free flowing silencers onto stock 28 pipes for another 1~1.5 horses. throw them away and fit TYGA's and get another 5 on top of that