Given that E2EE messengers usually require being run on a smartphone as primary device, my guess is that they are trying to push the last remaining non-app-and-web-only users to their messenger app.
I'm one of them and I don't like this.
I'm one of them and I don't like this.
The argument being that some assurances typically associated with E2EE (that "even we can't see what you're doing") are shakier without a disinterested third party serving the application to the user. If you have some target user `Mr. X`, and you operate the distribution of your app `Y`, you could theoretically serve them a malicious app that sidesteps E2EE. And since it's just a web app: the blast radius is much smaller than if you were to go through the whole update process with Google or Apple and have it distributed to all users.
Most people I know using FB messenger do so on desktop via facebook.com and the app on mobile. I don't see them removing the former any time soon but if the web only version still exists for mobile users perhaps that will go.