I just recently watch New Gate anime EP.8. The story went from Shin, the main protagonist, made his companion NPC at the start of the game, to her being the most beautiful person in the new fantasy world after Shin cleared the last boss. This story is an Isekai that take place after a death game (Like Sword Art Online) by summoning Shin to a 500 years time after the game setting. We're not talking about the anime here so let's move on.

I think, if your story needs to hold player's hands with a companion NPC like Navi in Legend of Zelda, or have AI NPC in the HUD system to give hints to players, and also have character customization, you might want to add NPC customization to that system. Especially, if the story emphasizes relationship between a player and the companion. However, doing this could take player away from your core game play. Plus, NPC conversation might get limited because you couldn't plan ahead of what the companion would look like.

So it might not worth the trouble of adding it in. But you can always get creative by letting it be and let player laugh at how irrelevent dialogue to the actual aesthetic is, that's how the meme is born anyway.