Auto position Pop Screen out
Problem: To be able compare UIX design with real app You have to manually move "pop screen out" window to corresponding position where your real app window is shown.
Solution: Add extra button to the window (somewhere similar to overlay "opacity" control you already have) which on click will analyze content (image) of current display in attempt to find position of the "best match" (by minimizing some kind of root mean square (RMS) error of Zeplin pixels vs the same size area on dispaly). As soon as position found, move the "pop screen" window there.
Nice to have: display on fly the current RMS error (probably normalized by square area).