Good point. Does the standard insist on the specified fonts, or are clients allowed to overrule them according to user prefs? If the latter, a fix is just an additional "book default" entry in the fonts menu.
(If the former, that's a lousy standard, right there)
The standard doesn't do anything about specific fonts. The standard DOES have facilities to set a font family, i.e. serif, sans-serif, fixed-width, etc.
It throws off formatting for a lot of books if you screw with that sort of thing. Which is what Apple is doing.
(If the former, that's a lousy standard, right there)