Wayland on the other hand does not. How and if clients can communicate with each other is considered out of the scope of the Wayland protocol, except a few exceptions (e.g. copy/paste) so it's up to the Wayland compositor. That's why there are already multiple different "APIs" to do screenshots on Wayland compositors, some more powerful some less, and not a single one is implemented by all major compositors - basically fragmentation hell. That's also why stuff like color pickers still don't work without tedious hacks (e.g. misusing some of the screenshot APIs).
Yes, that's a feature I have used many times in the past. If you want to sandbox an app, run it through a nested X server.
And for Windows, more than once I wrote stuff that captures or injects keystrokes globally. Being able to do this is a feature that lets you solve problems by making things more interoperable.
Flatpak does aggressively isolate apps from the OS though: http://docs.flatpak.org/en/latest/working-with-the-sandbox.h...
Flatpak has no X11 sandbox. Others, like Firejail, have attempted to create X11 sandboxes, but they've had holes (last I tested they had the X RECORD extension enabled, which has no use except being a keylogger), or broke valid applications / accessibility tools.
Wayland doesn't grant Wayland clients permission to those resources, but without further sandboxing and using technologies like Linux namespaces, AppArmor, SELinux, ... that's completely useless in itself. Wayland only makes it harder/impossible for trustworthy applications to do their job, while malicious applications just take one of the many other routes to get what they want.
What you described is exactly the paper of Flatpak, I think it even used SELinux for it. AFAIK, Flatpak with Wayland is a good way to sandbox apps on Linux.
With X11 on the other hand I can sandbox X11 clients I don't trust, thereby limiting them in what they can do, but other clients I do trust have the ability to do all sorts of great things so I can do my work efficiently. While not perfect, not even close, it's certainly better than not being allowed to do anything.