It's actually pretty common for readers not to be able to override some settings if they're specified in the book's stylesheet. As much as I loved the Sony 350, it also couldn't overwrite defined fonts even with your own stylesheet (and I never considered it a flaw of the Sony, it's just how readers work and what they're capable of). You had to edit the book's stylesheet to remove the font specific lines.
So it's something most of us are used to dealing with, Kobo readers are no different in that regard. And I'm happy just opening the problem book up in Sigil and deleting the lines that get in the way of how I like to read. Or use the modified plugin that dickloraine was nice enough to make changes to for the "quick and dirty" fix if you really don't want to open up the problem book.
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