Yamaha's response:
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Our pro studio type keyboards like the Motif simply have 16 Internal Parts and 3 Plug-in Parts, and you can assign any MIDI Channel to any Part. But the 9000PRO is a bit of a different beast, because even though it is at the top of the PSR line, it is an auto accompaniment keyboard designed for the home user with emphasis on ease -of-use. So instead of using the "Part" and "MIDI Channel" screens of the Motif (which tend to confuse and scare off PSR users), they made it so you just choose one of the sections (R1,2,3,L) for the Plug-in Board Part. If you press the [MIDI] button, select 'All Parts', press the [8v] button, set either R1,2,3,or L section to a desired MIDI Channel, the PLG150DR Board will respond if it is selected for that section. It is therefore assignable to any MIDI Channel, but you are correct in that it has to be via one of the R1,2,3, or L sections. However, this was part of the design and is not a bug. The operating system does not (recognize) the part type settings as some of our other keyboards and because of that could not be modified to do so. Hope this helps.

YCA Support
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If there was any doubt at all that Yamaha does not consider arranger keyboards to be professional-use keyboards, it should be laid to rest now. I feel like I've been patted on the head and told not to worry about unnecessary things like setting MIDI channels that might scare me...