I agree with your position that tags like epub should generally be seen as restrictive on this site. We have a slew of country-specific tags for exactly that reason, and I can't think of any reason reason to treat the document-format tags differently.
In practice, however, I don't think there's one answer to this, for the following reason: people asking questions don't use tags consistently. Many users pick tags to draw attention, rather than to limit answers. On some SE sites, that's actually the norm. Even on SO, answers like "don't use [some tool/library/method mentioned in the question] for this" are often appropriate and score highly. So, sometimes, a question is tagged with a restrictive tag, but context indicates the OP is open to answers not relevant to the tag. Other times, the tag isn't there, but the question indicates it should be. These, of course, are reasons why we have re-tagging edits and commenting on posts.
In your case, both your understandings were reasonable, but I think the best approach is to encourage the OP to remove a tag that incorrectly narrows the scope of possible answers. If the OP feels the tag is important, maybe there's a reason for that preference that would make a good edit to the question, such as, "I would prefer answers that deal with the EPUB format, but am open to others, as well."
