Usual non enchantable tools in the enchanting table dont work properly when they are assigned as primary items for enchantments, both custom and vanilla. 

There is provided a datapack with a custom enchantment, cleansing, for a brush. 
Notice how you can merge it with an enchanted book, yet the enchantment wont appear if the brush is placed in the enchanting table.

Note: in this datapack this applies for the brush, but this seems to be the case for shears, carrot on stick, and warped fungus on a stick.