Do Microsoft and Apple really want native apps? I've got the opposite impression: they've tried very hard to herd desktop apps into Apple Store model. Third party vendors, like Adobe, are also forcing clients to adopt subscription schemes.
Those are still native apps. I believe parent is comparing to bloated Electron crap that requires an entire Chromium instance to put a GUI on what is basically IRC and text editors.
Sorry I wasn't clear. The underlying problem is piracy. Big players like Adobe can still use the subscription model. For most vendors, the easiest choice is going the web route.
Deployment is another PITA that makes App Store model desirable for the vendors. For Apple and Microsoft it's even better because they get a cut, they curate their platforms and have the upper hand over vendors lest they become competition.