A little under 1/3 of Amazon book sales are ebooks, and it's becoming common for a print book to have a Kindle alternative. Having said that, it is also true that ebook sales as a percentage of overall sales are starting to flatten, so print is hardly going to go away.
Independent publishers want to have one platform to output both print and ebooks. After all, the content is the same. i haven't seen any numbers on this, but with my own buying habits, I see the great majority of ebooks are simple text books, some with photo sections, but rarely with photos that have to be in a certain place in relation to the text (outside of the cover and some chapter "numbers" that are images). Fixed layout books are important to certain market segments (kids books, graphic novels, etc.) but IMO remain relatively limited overall.
So reflowable ePub is very important. We should all remember the slow evolution of ePub support in ID, beginning with a very buggy implementation in CS5.5. Hopefully, we can expect better from Affinity/Serif (i.e. *not* buggy) and see solid ePub support roll-out in phases. I regularly edit ePubs using Sigil, fixing things ID did not get quite right. So if I had to do that with Publisher, I could live with it, particularly if I was taking care of things not yet supported by Publisher, rather than fixing buggy output.
Yes, once you touch the ebook with Sigil, you basically lose the ability to do updates with ID or Publisher. So yeah, I would like to see everything in Publisher at some point.