If tzara'at is a spiritual affliction that manifests physically due to lashon hara and the kohen must diagnose it by examining the person's skin, why does our tradition hold that we shouldn't judge others by external appearances, yet here the Torah seems to make spiritual status entirely dependent on what's visible on the outside?

You're making a fundamental mistake in your understanding. The Torah is not making spiritual status dependent on external appearances at all. Let me explain the difference clearly. When we say don't judge by external appearances, we mean don't look at someone's clothing, their physical features, their skin color, or how they present themselves and assume you know their spiritual level. A person can have a long beard and a black hat but be completely rotten inside. Someone else might look completely secular but have a pure neshama. The Gemara tells us that if a person's exterior doesn't match their interior, it would have been better if they were never born. Looks can be very deceiving, and we see this constantly in our generation. But tzara'at is completely different. This is not about judging someone based on normal physical appearance. Tzara'at is a supernatural disease that HaKadosh Baruch Hu Himself brings upon a person as a direct punishment for specific sins, primarily lashon hara. The physical manifestation IS the judgment from Shamayim. The kohen is not judging the person's character by looking at their skin. He is simply confirming what Hashem has already decreed by examining the specific signs that the Torah commands him to look for: the white hairs, the depth of the affliction, the specific discolorations. The kohen cannot even check himself for tzara'at. The Mishnah in Masechet Nega'im says clearly that a person can see all afflictions except his own. Why? Because a person does not see the deficiency in himself. Everyone thinks they're right, everyone thinks they're good. The kohen can expertly evaluate millions of people, but when it comes to himself, he's biased. This teaches us that we need objective Torah standards and experts to evaluate spiritual matters, not our own subjective judgment. The whole point of tzara'at is that Hashem is speaking to the person in a unique language. When someone gets tzara'at, there's no doctor that can cure it, no medicine, no blessing. The only cure is teshuva. Hashem gives this person the disease to force them to reflect: Why did I get this? What did I do wrong? And they have to do teshuva to be healed. This is Hashem's mercy, not cruelty. He's giving immediate feedback instead of letting the consequences of lashon hara destroy lives for twenty or thirty years. So there's no contradiction whatsoever. Not judging by external appearances means not assuming someone's spiritual level based on how they dress or look naturally. Tzara'at is Hashem making a supernatural physical sign to indicate His judgment and to bring the person to teshuva. The kohen is simply the spiritual doctor confirming what Heaven has already decreed. He's not making assumptions about character based on someone's looks. He's reading the Torah's diagnostic signs that reveal what Hashem has already determined about that person's spiritual state.