Tunnel Snakes Rule perk should recognize any default weapon and its variant as a same weapon. Having Wanda on yourself and Assault Rifle on Butch should increase the damage, and vice versa.
I'm not much familiar with script, so excuse my igonorance, but I can think of a way of make that happen by fiddling with weapon's repair list. Make it check if the weapons of the player and Butch fall under the same repair list or not, since most weapons' repair list consist of its normal and unique variant.
Armor on the other hand, their repair list isn't as straight forward and consistent as weapon's, so 'same armor' feature should be left as it is.
Since Tunnel Snakes Rule relies on having to re-arm and re-dress Butch's equipment however the players want in order to be benefited by it, I believe Butch's behavior (which does not limited only to him, but to all NPC) of preferring the best weapon and armor he has should also be tweaked as well. As of right now, I cannot make him equip Combat Shotgun without having to remove his default 10mm Pistol through the usage of console command. I don't know if this would be possible, however.
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