In my experience with MIDI routing each keyboard should be treated as a separate device with its own separate 16 MIDI chanels. This way you can continue to run your controller in omni. Your host should be able to localize these omni messages to differentiate them from the other ins/outs. Unfortunately I have very limited experience of running MIDI in Logic and they may have there own weird way of doing things because Logic is like that. I will have a look as soon as I am able and will get back to you.
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