Qayin said:
The narrator for PM1 even asks how Kammy got there. And PM1 had plenty of paper moments (Mario and Goombario falling off a cliff over to take no damage since they're paper, King Goomba's fort being a cheap prop, the Trojan Bowser). If anything, it was Thousand Year Door that tried to move away from the "Mario In A Paper World" depiction with the curses.
All of those except for Mario and Goompa falling are jokes/simplifications. After the intro, the storybook angle is never brought up again, Goomba King's fort might as well have had a button simply activate the bridge and a Trojan Bowser isn't a paper-related concept.
They could have just redesigned him to stand out more ala Super Princess Peach.
Super Princess Peach's case was more of a transformation. I don't recall too many instances in which a main series character was redesigned for an RPG which wasn't a transformation.
Bowser has had plenty of games without an obvious right-hand man. And even when he has one from Sunshine onward he's had Bowser Jr. over Kamek or Kammy.
The entire point of Bowser having a right-hand man is that it's someone to oversee things for him (hence Bowser doesn't have to fly out to put the traps in Shy Guy's Toy Box or whatever) especially in an RPG and with him using his army. It helps with build-up since you can only confront him directly at the end (though it backfired with Sticker Star to the point that Kamek had more presence than him).
Bowser Jr. isn't really portrayed as Bowser's right-hand man nowadays outside of Mario Party and the sports games. In the 3D games, Boom Boom and Pom Pom fill that role after Galaxy, Bowser spent most of NSMB "dead" and Junior + the Koopalings mostly did everything with Bowser only getting involved at the end of Wii. In fact, in the RPGs in which Junior shows up, he's usually off doing his own thing (Sticker Star, Paper Jam, Puzzle & Dragons) while Kamek is portrayed as the right-hand man (Dream Team, Paper Jam, Sticker Star).
I haven't heard anything about all the mentions being Western only. And Sticker Star isn't all that out-of-place with PM1, at least. That's the point.
I'm not sure myself anymore: The wiki doesn't mention it, but TVtropes has a note that it's only in the US version. I have no way of verifying which is correct, so I'll just assume I made a mistake.
Even so that's two small references. And the very fact that the characters are self-aware of their nature of being paper, something that was rarely mentioned even counting the 4th wall breaks, already makes it out of place. Then you have stuff like the existence of the Things, the design of Mario's House in Color Splash despite the house remaining consistent in the first 3 games, all the Toads looking alike, etc.