I think you have lost the point of the Crop:Rectangle filter. You can crop your video to get rid off the black in the background. To remove the black, what you need to do is in the Crop: Retangle filter, set Padding Color, his alpha channel to a value equal 0, so you will only see the rectangle you have selected with the clipping (crop filter)
And the second qu estion: you need to cut the video on each photo and then apply the crop on each piece.
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