I don't know if the transmission/shaft drive gear whine is excessive, but it was one of the first things I noticed on the Trophy. It is very much there all the time, and sounds a lot like the old Mini gear whine. I wear ear plugs all the time, so it does not seem too much, just something to get used to. I also initially found the engine to be more mechanical than I was used to on the ST1100, but am used to it now. I don't mind at all the way the whole drivetrain package works in the real world.
I found putting on a slip on pipe (staintune) seems to balance out the engine/shaft noises quite nicely.