I don't know how to make it use something other than a normal bomb as its proximity weapon, because I don't quite understand how its misc 2 value is supposed to work.
Here's what it says:
Seriously, no matter what I set it to, the Bombchu is still using the normal bomb as a proximity weapon!Misc2: If Misc1 is 1, specifies the weapon to use when in close proximity to Link. This value is treated as an offset which is added to the enemy's ordinary weapon to obtain the proximity weapon.
EDIT: I have reported this issue in the Open Beta Bugs.