Wouldn't rootless chord recognition imply you AREN'T playing bass?!
I would imagine, as picky about the inversion you are using as this is (it's why I'm not a big fan of the feature, which isn't on Roland's anyway), you would have to have the chord recognition in the top half ONLY, or the lower note might upset the recognition of the chord (mind you, I don't have a Yamaha, so I could be wrong... Ian? Scott?).
This would be awesome if you could split the keyboard in THREE, or have a rootless mode that only triggered with a three note input (like Pianostyle Mode), so you could still solo on top...