I grabbed a copy of "Jonathan Strange and Mr Norrell" from my library via Overdrive and, off-hand, except for what they've done with footnotes on the chapter names (it's just something new to me), it looks like most things should be fine with it.
I can see some of the footnotes are long, so they might not get a popup. But, they do all have to/from id/hrefs, so navigating should work simply as links.
I see some of the poems you mentioned and I worry about them. They do have formatting classes applied to the lines, but each line is a <p> and the initial link to the footnote is also a <p> and I'm pretty sure that first line is where the footnote officially ends. So, I'd guess that the popup for that will only show the first line. Of course, since I've seen the footnote text in the popup windows just continue on until an <hr/> or new chapter mark (instead of ending with the closing footnote block tag), I could very well be wrong about that. I think I'd try changing the first <p> there to a <div> and including all the poem <p> lines inside the <div></div> pair.