What exactly is the difference between using the Citra provided in the texture pack, or using another Citra?

I was thinking of maybe using a single Citra, because currently I have like 3 Citras; the Citra from the Ocarina of Time texture pack, the one for Majora's Mask, and my regular Citra for the rest of the games.

If I move just the textures to my own Citra, will there be any noticeable difference between using my Citra and not using the one from the texture pack?

Is there a downside to not moving the whole User folder from the texture pack?