A PDF should be more than a facsimile of a print product.
I agree with that, but only a bit. There are a few things beyond print that should be provided: Providing bookmarks and making sure the text is searchable and copyable.
But the one reason for choosing PDF is that it is the best digital format for print products. Sure it has lots of digital features. If you’re really serious about making an digital product, however, you should be looking beyond PDF.
Of course, other formats have their issues. Sometimes people come back to PDF because that print-basis makes it seem more mature, which arguably it is. But, if you’re trying to move beyond print, you need to move beyond a format with such a heavy print bias.