Well, one of the primary differences would be, on the regular tempo, the jazz guitarist is probably playing 1/4 notes. When you cut to double time, he's probably playing the upbeats. Similar things will happen to any piano part in the style, and horn lines etc..
You are right that it is primarily the bass and drummer that will go crazy!
So, either you've got to stitch a style together out of one style at normal and another at double tempo (and it's often hard to find a 'true' double tempo at the same clock speed as the half times, so unless the Yamaha's allow you to have different tempos for Variations in the same style (don't think they do), you might have to do some serious MIDI editing to get this to happen (Cubase, for instance, has a 'half time/double time' command that will create double time out of a slower pattern without you having to change the tempo) but it seems like a lot of work.
I think I'd still go with the two Registrations, myself, if you can't find a style that has already done the grunt work for you...
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An arranger is just a tool. What matters is what you build with it..!