Both units are incapable of remapping their MIDI messages to suit the other. Plus the 3K's MIDI implementation is pretty barebones. Yamaha and Roland's drum mapping are not on the same page entirely (Yamaha's fault here, GM was already a de facto standard when Yamaha decided they knew better...). And from what I've been told here several times, the 3k's MIDI out is a kind of 'all or nothing' affair, you can't pick and choose which Parts get sent and which don't.
Sadly, there aren't many arrangers where MIDI compatibility with other gear, and especially other gear from other manufacturers is given much priority at all. Korg seem the best at it, Roland a bit behind them, but Yamaha trails quite a bit behind. As Ian will no doubt jump in and say, these things are designed for HOME players... How DARE we try to use them for anything more complex!
Makes you wonder why they even bother to put a MIDI jack on the darn things any more (in fact, Yamaha DON'T on some of their low end ones) if the OS is so crippled as to make its' use moot...
This isn't a Yamaha bash, BTW. I believe that ALL arrangers could have MUCH better MIDI implementation than they do now, with the possible exception of Korg...