1) people are running all kinds of applications on Linux, not just open source ones. The solution has to work with Siemens NX or Autodesk Maya just like it works with Gtk Demo.
2) Even if you can modify apps, are you going to modify them all? No, most of them would be never fixed.
3) so you are mistaking "we get to modify apps" with "we get to rebuild the world, and everyone's system is part of the rebuild".
Applications which are extremely performance critical and accuracy-critical, where the compositor shouldn’t touch rendered pixels at all? Yeah, that works great, right?
We can just enforce the functionality in all new toolkits and deprecate old ones. Existing, old software will just render badly, like it does today, and everything new or updated will get all the advantages.
We can even enforce a new Wayland2 protocol, everything old can just render through XWayland as a blurry mess, Gtk3/4 included (they do support X still after all), and everything new can use the improved protocol immediately.
That's not how open source works. We get to modify apps. That's the whole point.