One more great thing about Korg, they let you calibrate the pedals so it is possible to have more options in choosing pedals.
Having said that, I've never had a problem using most pedals with Yamaha. At least you can change the polarity and assign any function to any of the pedal positions.
Korg has one programmable, one dedicated to sustain, one to volume. Their EC5 lightweight, inexpensive foot controller is great though, so even more options.
Yamaha's only option seems to be that heavy, expensive thing (MFC10), unless you want to get a third party foot controller and try to program it properly.