Create a second version of your video source by "copy", then "paste (reference)"
Move the instance on top into a group. Only the one on top, not both.
Crop the instance in the group by dragging its window handles while holding down the ALT key to match your desired outline of the part that should have the chroma key filter. You can also add the crop filter to the group to crop, but make sure you add the filter to the group and not directly to the instance. If you need a custom shaped mask instead of just cropping, don't crop. Instead, add the Image Mask/Blend filter to the group and assign an appropriate image mask *.png file.
Finally, add the chroma key filter to the group (not to the instance, this would reflect the filter to both instances) and configure the color matching appropriately.
Now you have 2 instances of your camera, one original and one cropped and chroma keyed. Make sure the original is below the group with the filtered instance (but not within the group), so the filtered instance will overlay the original one for the parts you want.