[nh2]

Try

    sleep 2 && zenity --entry --text="Enter text:"

and switch to a different workspace where you start typing.

The popup of the other program should appear and capture your input.

As far as I know, i3 has no prevention for that.

(In this example I'm spawning a program delayed to demonstrate that, but the same can happen to e.g. the gpg-agent password prompt popping up when an SSH connection that uses it reconnects, a chat window from an IM program, and so on. I think the idea of Wayland window activation / focus stealing prevention is that you can still have those windows pop up, but without them taking your input.)