[Varyon]

Personally, I wouldn't have a problem with the bonus from Weapon Bond increasing your damage with a weapon for which you also have Weapon Master. It's quite the edge case - the chance someone will have Weapon Master, yet not be sufficiently skilled with their favorite weapon for the full bonus, strikes me as low (it would likely only show up if forced to use the weapon with a different skill than usual, such as a katana-user who favors Two-Handed Sword finding himself having to rely on the -4 default to Broadsword) - but by the Wendler-Dell'Orto Rule of Awesome*, having a character deal more damage with their favorite weapon is quite acceptable. I could have sworn there was a Power-Up in DF to get this anyway (essentially importing DnD's Weapon Specialization Class Feature), but can't find it; presumably, it would have Weapon Bond as a Prerequisite, and be built as something like Striking ST (Single Weapon -60%) [2]/level.

*From Pyramid #3/44. "Anything that enhances the potential for something to be Awesome is good. If what you’re doing isn’t Awesome, stop doing it and do something else."