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I think it has something to do with The Noise's bombs counting as the gun, like in the Vigilante's fight were it starts without him giving you the gun.
I actually messed with this the day it was posted, without being aware that this was posted. Also, if you restart the level, it corrects to the proper fight for the character, changing the music and stuff to normal (Noise for Peppino and Doise for Noise)
If you do the Doise fight and switch to Peppino with debug (not in swap mode) The game will make Peppino have a gun that doesn't hurt the Doise at all.
Really interesting how the Noiseys in the background have a dedicated Doise palette despite not showing up in the fight (unless they use the same palette as The Doise's background)