But what about pop ups that come from within the application? Anything that has dialogues come up when there is a chance the user might be using enter/return for a different purpose is a bit crap, especially with multi-screen systems where there is a fair chance the user is looking elsewhere. Even just having no pre-selected default would help (so arrow - enter/return would be needed).

Is this an example of what you have in mind: The user is typing at Microsoft Word, and it's not a keyboard shortcut to open the "document properties" window, and Microsoft Word chooses to open another window during the typing and divert keyboard focus there?

I think so, yes. Diverting keyboard focus in the middle of anything should never happen. Should there any exception to this?

This seems like something that should be handled by the application's developer. A different application's popup or focus steal should be managed by the window manager / OS.