Well, web apps could kill their desktop platform because you can have the same experience cross-platform, so why buy a Mac? It's in their interests to ensure that the Mac app is substantially better than the web app by integrating more deeply into the OS. So offering a single framework that can do a great job on web apps and an excellent job on Apple platforms, you ensure that it's the most attractive option to developers who would otherwise build an Electron app. And you ensure that most cross-platform apps (which is most apps) are better on Apple platforms.
(If they get there first, this has a side benefit of preventing Windows, Linux and Chrome OS from doing the same thing as easily.)
That's weird. Why did they say that web apps were the way to go for the first two revs of "iPhone OS"?
But seriously: app store revenue is a rounding error. It's more likely that Apple perceives web apps as a threat to their bottom line the same way they view ripped MP3s as a threat to their iTunes revenue.
In 2018 AppStore revenue was $46.6 billion [1]. Apple revenue for 2018 was $265.6 billion [2]
So, your "rounding error" is in reality 17.5% of Apple's entire revenue. It's "only" twice bigger than the entire Mac portion of Apple's business which is $25 billion [3]
(If they get there first, this has a side benefit of preventing Windows, Linux and Chrome OS from doing the same thing as easily.)