The wpa_passphrase tool simply stores the raw hash used by WPA to authenticate to the AP. This is the behavior performed under the hood even when the plaintext

The wpa_passphrase tool simply stores the raw hash used by WPA to authenticate to the AP. This is the behavior performed under the hood even when the plaintext is utilized. You could still reuse the stored hash to maintain the same level of access afforded by the plaintext passphrase, but wpa_passphrase isn't security theater or obfuscation.