If you use FBReader (the default reader) then your font selection applies to all formats and all ebooks.
I was not able to get the alternative reader, CoolReader, to work. A long press of an FB2 ebook number brought up a menu, but it only lists FBReader as a reading option. CoolReader is what is used for FB2 under the standard firmware, and it used to be available as an option for OpenInkPot.
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