Yeah I can definitely clear that up. In the actual game Junker only uses outside of Bowser enemies and traditional Mario enemies: specifically Scutlets, Bob-ombs, Cheep Cheeps, Chain Chomps, Wet Bones, Nooz and Thwomps (all of which have browner palettes besides Nooz and Wet Bones). When the Junker Cans switch Luigi it seems the game uses at random any small enemy in the game outside of Bowser, but none of them have altered palettes. There could be Inside Bowser enemies during that move but I haven't seen it during the entirety of my attempts at a Challenge Medal Junker, plus their palettes wouldn't be altered and it wouldn't make a lot of sense in-universe.

So about that, I have tried a couple of times to see where these are used in Junkers fight but they seem to be deactivated? They are stored in the same place as all of Junkers attacks. If you did see this then could you send me a video of that of that or a screenshot? You might also be thinking of the brown Scutlet from Junkers trash attack maybe?

aren't these in Junker's fight?