Bolting everything to the engine means lighter weight. It allows one to isolates loads/jobs. The weight of the rider on the seat is handled by a very light frame, a frame that doesn't have to deal with forces from the rear wheel shocks. And with the rear swing arm attached directly to the transmission, which is built into the engine block, nothing is wobbling around. But to do this you need a well-balanced engine. Watch any harley accelerate. It's engine is bouncing around on soft mounts.
Here is the definitive japanese sportbike, the honda CRB600. The last pic is "naked", ie without the plastic fairings and "birdcage" that holds the instrument cluster and windscreen. Look at how tightly integrated everything is. You don't normally get engineering like that in a vehicle selling for only 12k. Chances are you can pick up a slightly used one for 6k.