How long before an app will actually delete your file when you say "Open..."? Sure that could happen, but why would anyone do that? And especially in a open source world where anyone could just fix/improve it?
On the other hand you say that the position of the window decorations is important, while I'm much more affected by GTK apps not *behaving* like they should within KDE for example. Still, it's something we all learned to live with. I think it's the same with Wayland, things will either get fixed or we will learn to accept them.