Weird. I've experienced the issue with various apps getting upset when another one is displaying over it. I like to have a little YouTube video playing in a popout and some buttons will refuse to press when this is present. I can't imagine this plays well will magnifiers or other assistive tech, but I understand their worry that a malicious developer could contrive to make you click a wrong button by covering the relevant context.

As for getting upset about sharing a phone with unapproved apps, I think this is a failure of sandboxing. The app should see as much of the phone as I want it to and no more.