The Weapon Master and Weapon Bond modifiers weren't appearing in the modifiers listings for weapons, because they were in a modifier group that wasn't referenced by the weapons.
The easiest fix was to change the <Weapon> modifier group to <_Weapon> so that GCA would see it as a globally applicable group, and make it available to all the things through the drop-down.
So, that's what I've done for now.
Here's the new
Dungeon Fantasy RPG.gdf file.
You'll have to load this new file, then any existing characters will need to resync their Equipment (and the stuff on the left side of the dialog).
Once that's done, in the Modifiers dialog, you should see
_Weapon in the drop-down list, and that's where the
_Advantage: Weapon Master Damage Bonus and
_Perk: Weapon Bond modifiers will appear.