That's my bad! It's inconsistent/unclear and that's a mistake.
The ending of the Ruthless route and the Hinterlands were written months after each other and by different hands so a few details and explanations weren't coordinated perfectly. We might go back to fix this eventually.
I do have a few rules for how the charms work in this situation, though. As a rule of thumb, if you've spent a good amount of time with a mythical when he wasn't wearing a charm you can see their true shape even when they're wearing a charm. Keeping in mind that charms only affect perception, it's basically that your brain gets so used to their real shape that it overcomes the illusion. Still, if you strain your eyes and make an effort you can still see their human form, kind of like tricking yourself into seeing an optical illusion in a different way.
So... P can notice on his own that Storm's charm is malfunctioning, it just takes a bit of effort. It's easier for him to just ask Storm to check it. That's the explanation for the inconsistencies you noticed.
We didn't touch on it as well as I wanted to but P's feathers make him capable of seeing through most charms, period. It's hard for any but the best charms to trick over a hundred supernatural eyes simultaneously. This also means that any mythical that P meets whose charm tricks him is packing some serious power.
Another detail is that, yes, the fact P made Storm's charm means that P can always see Storm's true shape, but that goes both ways. Storm can always see P's real shape as well.