I had a Yamaha (IIRC) for my 2005 Pilot. (Never used it as it had that much room inside). The problem you will find is that with Honda's roof rack design now, you cannot mount anything to the roof without buying the additional cross bars. In my old Pilot (as well as many other vehicles) the roof rails had a gap between them and the roof so you could attach things without having the cross bars.
As to bags. The Yamaha seemed good quality, just never needed it.