Yes, that's the flaw in the method. Using the B Output wreaks havoc on all your other programs. And if you process each layer differently, as I do, then you also get imbalances in layer volume levels. That was, in part, my reasoning in having two Prophet '08 Keyboards. It's too complicated to continuously go back and forth with the output set up, so I leave the top instrument in that set up permanently, which makes an excellent mono synth, but at a poly synth price tag.
Thanks for the LFO tip!
I think you'll really like being able to program a different effect into each layer of the Rev2. It quickly makes most patches better. I also think you'll like being able to vary the width of all the waveforms, especially given how much you utilize waveshape modulation with pulse/square waves. The sub oscillator is also a nice addition; I like to dial in just a touch in order to add a little thickness to leads.
As I said, I'm using the B outputs, and so I adjusted most of my patches to put the same patch on both layers, which sounds fantastic. I'm trying to decide how much I miss having that extra layer and whether or not I need to get a Rev2 module. Most of the time I don't miss the extra layer, but of course that's a big feature to be without. At this point, I value the stereo spread more than I miss the extra layer.