I think Appearance → Logo was added when many settings were grouped into config pages and made directly accessible in the admin sidebar. So, I think this is kind of the place where it should be easier for admins to configure that because it’s a separate place compared to it being hidden in all site settings. But in the end, it just looks a little different, but you edit the same site settings. Most site settings are also part of one of the config pages.
I reported before that the hints on which size each logo should be differ between site settings and config page. This also makes it more confusing.