Are you sure that's canon?
It doesn't really match their in-game descriptions, and other comics feature questionable things like a Waddle Doo having a 3DS system.
I haven't got a clue if it's canonical, but it's still official promotional literature that's clearly intended to explain this particular one-off game-mechanic (I never bought the game as it never interested me).
I had to look up the in-game figurine
descriptions, and from what I can see, there's nothing about those descriptions that suggests that Bandana Waddle Dee is multiple individuals or that his case is a Toad-like case - the promotional comic slots right in with the descriptions, in spite of its humour, it seems.
Indeed, seeing that the content in Rainbow Curse doesn't appear to contradict Bandana Waddle Dee being depicted as one unique individual, and that this was done for the sake of a gameplay mechanic that occurred in one side-game, coupled with the fact that they produced promotional literature to differentiate the two additional alternate-coloured versions, it suggests that his is absolutely not a Toad case.
As an aside, I will say that it doesn't help that, at the time of Kirby and the Rainbow Curse, they hadn't settled on which name to use for Bandana Waddle Dee, which muddies the waters with the names of the figurines, and which has no doubt caused some confusion out there at some point. They were literally changing between Bandana Waddle Dee and "Waddle Dee" every other game, at that point, before finally settling on Bandana Waddle Dee and now sticking with it.
Still, there's nothing questionable about a Waddle Doo having a 3DS, though, unless the reason is that he can't use the 3D feature.
Multiple games have shown Kirby and Bandana Waddle Dee playing DSes and 3DSes together, after all, and Kirby Super Deluxe featured an accurate representation of the then-current version of MacOS as one of its bosses.