The only way I know of is with ffmpeg, but the syntax is incredibly tedious and time-consuming to create: you need to type in the rectangle in pixels, and the start/stop time in seconds. To do it for one across the whole video is awful:
-vf "delogo= x=1640 :y=3 :w=270 :h=90 :show=1"
but to do more than one, or to add start and stop times, it's completely bonkers:
-vf "delogo= x=60 :y=310 :w=180 :h=120 :show=1
:enable='if(between(t, 11, 22), 1, between(t, 219, 231))'"
(And you can't type those seconds as H:MM:SS, either.) I just want to drag out a rectangle with my mouse, and select the range on a time slider. Why is this too much to ask?
(And obviously I want this hypothetical tool to automatically recognize them, too. ENHANCE! ENHANCE!)