The short answer is yes.
As I suspect others also are curious about this, the slightly longer answer is:
I don’t know the fb2 format, but we have put down a lot of time and energy to make this as flexible and powerful as possible – but you will have to provide the templates.
And on the template and URL side of this, you should be fully covered, but it is important to know that on the content file side of it, you are still limited to Blackfriday, MMark, Asciidoctor, HTML etc., which I guess mostly still produces HTML.
So when creating your e-book templates etc., that is something to think about. But in addition to Content (HTML, mostly), there are also RawContent (markdown, mostly) or Plain content versions that could be used.
We will improve in this area, but it would be good to see it in use a little first. I know we have to fix the issue below to make Hugo perfect for AMP pages, as one example: