The X11 connection is generally an enormous hole in such containment, but yes. Such containment definitely helps. That is why I run as many applications as possible as Flatpaks, as they employ similar countermeasures, and why they’re playing an increasingly big role in modern distros.
And it’s great that you’re risk averse and able to avoid untrusted scripts to that degree. It’s just not feasible for the general user, which is why things need to be secure even if a malicious script is mistakenly allowed to execute.
I’m not saying that that specific annoyance is a security measure. I’m saying that the whole paradigm shift that Wayland is is partially motivated by improving security. Such paradigm shifts come with paper cuts, especially in the beginning. But the rough edges are being filed down one by one. That’s not to say that Wayland is the answer for everyone yet, nor that it will ever be. There’ll always be exceptions. But for the vast majority of users it is, and it helps keep their systems safer than they are without it.