Absolutely, I can see this being an issue for Extensions that rely heavily on fixed/absolute positioned elements. Long term, this will most likely be addressed by allowing you to provide a pop out specific view, like you can for mobile.
The scenario you described in video extensions is a good case for why we’ll need a solution for this before we rollout for all Extension types. Plenty of overlays, if not most, do not have interfaces that map directly to a pop out.
Yes, the new window’s initial dimensions will match the size of the Extension on the channel page.