I see that the title is to catch the readers rather than actually to state the end of native apps, if you admit that they "still have a few capabilities that mobile apps will not have for a potentially long time".
It's not that device manufacturers have never tried the "all-web-tech" road in the past - it's an effort as old as WebOS - but there are apps which are *explicitely* thought for devices, and aren't suit to live on the web in any form. Like a file explorer, for example.
Honestly I have no idea native apps are doomed, or even will be relegated in a small niche. In my opinion, it's way too soon to tell. We still don't know if PWAs will ever catch on, among developers *and* users. Safari doesn't even support service workers at the moment.
One thing, for sure, is that we should try to develop PWAs because they *do* look cool!