Hello!
I am using ‘Magneta’ font, but when I choose ‘book’, ‘thin’ font-weight, shortcut for bold and Italic doesn’t work. 
When a font family has lots of weights, as Magneta does, the effects (if any) of command B and command I depend on how the font designer organized the family.
I don’t have Magneta myself, but it has plain and italic versions in six weights: thin, book, medium, semibold, bold, and black. It might be set up so that command I sends you back and forth between plain and italic of a given weight, while command B sends you back and forth between the book weight and the bold weight, having no effect at all on any of the other weights. Other arrangements are possible; the only way to tell is to experiment with a particular font.
This is all up to the font designer, Scrivener has nothing to do with it.