Baraag is way more permissive than misskey.io and it gained a pretty bad reputation in the past because of that, plus it essentially advertises itself as a safe haven for lolicon art, so that’s why it’s on many block lists.

misskey.io is just a generalist Japanese instance. It’s also the biggest misskey instance and is run my the main developer, so it’s usually not blocked by default because most people use it.