If they got decently paid, by allowing proprietary apps, one of the competing apps could stick around by virtue of actually making money.

The ElementaryOS company would also get more cash, and could, (like Apple!) improve a core set of apps.

A "kernel" of good quality Linux apps could also spread to other distributions, and hopefully slowly coalesce around GTK and "ElementaryOS" style GUI as a de-facto standard. (Since the other distros are more accepting of jumbled GUI styles anyway, why not make your app on ElementaryOS first, and distribute that version on the other Linux versions, too.)

Anyway, the hurdle is not technical - flatpaks or no flatpaks. The hurdle is strategy and ideology.