I thought Instapaper scraped the page and stored that, to accommodate sites that require login for access. So not trivial to just re-download the articles. Plus the whole point is to have them available when you're offline.
I'd say in this case, the content is user-generated and should be backed up.
That's a tough line to argue: the scraped page is actually stored by Instapaper (otherwise you could not access it from the website), so you re-download it from there, and technically it's not user-generated it's at best user-curated.
But this does indeed defeat the point of having it offline, which is a significant part of IP's purpose.
I'd say in this case, the content is user-generated and should be backed up.