EPU:
I should preface my remarks with a disclaimer - I'm fairly new to all this, and have had very limited experience. I have no experience with the units you mention. However, such things never stopped me before!
My understanding is that the number of channels available is limited only by the controller/sequencer's ability to address them separately. I'm using a very crude computer program, so I'm stuck with 16, but others have no such limitations.
I have read that SysEx messages can even be used to divide up channels between different units of the same manufacture, or even same model. I've also been advised (in this forum) that when you intend to patch to different units, it's a good idea to have a MIDI mixer module which can route different channels (or even specific signals in one channel) along one of several MIDI outs. That is how I intend to go, and have the unit on order.
In my way of thinking, it wouldn't make sense to divide alternating notes of one voice between two synths or synth modules - it would make more sense to split up which modules get all of each patch, thereby making voices uniform in sound, taking advantages of the best voices of each module, and still reaping the harvest of reduced MIDI traffic to each.
Hope this helps. I've found that your concerns are very legitimate, since I'm finding it's pretty easy to overwhelm my little JV1010.