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There are really two options:
a) if an object is a container, and the contained is accessible to reflection (preferably through gc.get_referents), then the container shouldn't account for the size of the contained.
b) if the contained is not accessible (except for sys.get_objects() in a debug build), then the container should provide the total sum.
A memory debugger is supposed to find all objects (e.g. through gc.get_objects, and gc.get_referents), eliminate duplicate references, and then apply sys.getsizeof for each object. This should then not leave out any memory, and not count any memory twice.