Those annoying pop ups are only annoying because on day one everything has to ask permission. After that, you only see them if you install a new application. I certainly prefer having to give my permission before an application uses my microphone or records my screen.
I agree with “just day one” in general, but do note that if you develop apps or write AppleScript that require permissions it can get pretty annoying as every build asks for permissions all over again. (Actually I’m not quite sure about native apps built from Xcode, but this was my experience with a Qt app I wrote last month.)
