Your muffler guy is correct Ken J; if the mufflers can be securely attached to the engine and if it is convenient to do so, go for it. BUT, the plumbing ought not to be rigid: Use a couple of the one-piece muffler tubing ball joints manufactured by Ken Brock.

There is a broad spectrum of vibration created by the engine-propeller combination; the individual cylinders firing; the propeller blade passage past turbulence generating obstructions and perhaps the redrive itself. More likely than not, there will be a frequency present that will resonate with a natural frequency of the exhaust system. The ball joints isolate and dampen the vibration. Ball joints must be lubricated with a high temperature lubricant such as Blue Molly, available from any industrial power transmissions products dealer; otherwise they will weld themselves together. There is another high temperature anti-seize compound sold at auto supply stores called Copper-Eeze or something like that which will work as well.

The Rotax 912 S Installation manual on page 10-1 says that the minimum bending radius, at the centerline of the pipe is 1.6".