What is the popup you're encountering? Because it sounds like a bug, and I'd like to make sure someone is working on fixing it (or has already done so).
I just tried to reproduce it, and it doesn't seem to actually happen for every new window I open, so I am not sure what I am doing to trigger it, but I do encounter it several times a day.
edit: Incognito seems to do it, which makes sense because I often enter/leave incognito to make sure I have a fresh cache & no cookies when testing.
The custom extension popup, and you dont want to fix it(status is wontfix) ,where a simple checkbox in the settings could have fixd it... you made our lives miserable.