I don’t know if I fully understand the problem but here some info that might help:
Quicktime has differnet pixel aspect ratios as well as different frame aspect ratios.
16:9 and 4:3 Quicktime movies have the same number of pixels, but in the 4:3 movie the pixels are 0.9 pixel aspect ratio (normal) , in the 16:9 clip they are 1.2 pixel aspect ratio (anamorphic). That’s why there’s an “anamorphic” tick box for each of the clips in your bins.
Computers use square pixels to display Quicktime files so 4:3 will look pretty much normal but 16:9 will look more squished. I think when you export movies from FCP they are supposed to have a flag that tells other programs whether they have normal or anamorphic pixels. What’s important is when you re-import those files into another software like after effects or if you make frame grabs, make sure that the info has passed over. In After Effects, sometimes you have to ‘interpret footage’ which is basically where you set whether a source file has normal or anamorphic pixels.
Hope this helps!