It does not bother me that parts of Judaism and Jewish life consider Jewish souls superior. Every group at heart thinks it’s group is superior, the very center of the world.
I don’t think Jews are different in this respect from the Japanese, Chinese, Germans, English, etc.
I don’t think this ethnocentrism is a bad thing. You should think your group is superior and rack your mind to find ways that your people outdo all others.
The stronger your group identity, the more likely you are to think negatively about outsiders. This is a universal law, it applies equally to Jews and gentiles.
I don’t think Jews need to duck or hide from these statements. Instead, we should place them in the context of universal human proclivities.