This seems to be a really important question out there and I'm somewhat scared by the silence on HN about this. The silence makes me think that folks are going "oh shit!" with frozen fingers.
It does looks like the incentives are aligned in the direction laid out in the article. Companies can better control their user experience on mobile through uncrawlable apps. You hear "mobile first" a lot these days. These things are with users for longer than desktops/laptops. Anyone can carve out a section of the web where content gets created, but cannot be linked to.
The two gaps I see are -
a) mobile devices are good for _consumption_, but are not yet on par with *tops for _creation_, and
b) reputation systems on the internet (currently) require linking, and there's nothing to replace that in the mobile world.