Hi,
Have you tried to launch your game with debug option for collision boxes? Then you should be able to see if collision boxes are actually offset or they are fine, but collision is not detected for some reason.
I don't have much experience with godot collisons, but that would be first thing I would try.
There is "debugging" menu at the top where you can turn on collision boxes rendering. As I know it also show when hit is detected. Maybe that will help you or at least give some additional information.
I assume you didn't tried that since image you attached didn't include collision boxes displayed, but maybe I'm wrong.