Import alignment query compared to iphoto

HI, on Capture Pro 16, I'm importing two images, exactly the same object in each and in the second a person is present.  This is so that the person appears as if by magic in the second image.  This works perfectly well in iphotos but when I import into C1 the alignment changes and it becomes a bit of a nightmare to realign.  As I have over 400 images with this requirement and different objects (total 800 downselected) i would appreciate any advice on (a) understanding why there's a difference in image alignment when importing and (b) which tools can help me align an object in 2 adjacent images.  thanks so much.