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Every device works in a different way, I don't think that there are standards regarding the programming of the software that they are equipped with.
Besides that, almost every e-reading device and software allow some form of user customization over the display of the text, and AFAIK, you can't prevent this by coding inside the ebook. If you use styles that serve some functional purpose and not just for aesthetics (like your example, to differentiate between different kind of notes), your best option is to add a disclaimer on the first pages stating that if the user chooses to apply his customization, the intended experience/functionality can be compromised.
Usually the ereader, to know how to display the text, looks for these things in this order:
User customization of the ereader
Styles as defined in the CSS inside the ebook
The default ereader settings
Furthermore, keep in mind that often ebooks are read on B&W eink devices that can't display colored text.
If you need to differentiate between, i.e., author's notes and editor's notes, I would use some kind of abbreviation like A.N. and E.N, or a different font style setting (i.e. normal and italic, a different font), and with a disclaimer like said before.
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