Forgot name, but you know it's me.>>33325966>TotT
Limitations imposed by a Pokémon’s physiology provide an excellent opportunity for developing a unique character. Presuming Pokémon are reasonably intelligent creatures, it's foreseeable they have developed ways to deal with pesky "human obstacles" to get what they need. That's when the author is put in the hot seat; can the concept spur the imagination well enough to pass muster in the reader's eyes? Even if it requires suspension of disbelief, half of the battle is already won if you can preemptively articulate a setting in which this method chosen would work.
Secondly, describing how a Pokémon might struggle is part of the overall tone of the story. If you go for realism, then yes, a Pokémon might have a hell of a time opening a door if it only has wings. But if your story’s message includes the theme of overcoming adversity, then figuring out a way past that (strictly physical, in absolutely no way whatsoever metaphorical) door and thereby move the story forward is as significant as overcoming the regional champion at the end.
I don't write PMD, so I'm not qualified to respond on the challenge rating plus prong. I would imagine a similar approach would suffice. Construct the world, anticipate the challenges, and have the reader's imagination place things in their rightful place.