Yes, new instances usually automatically federate with everything. From what I've heard, there are "default" blocklists being maintained as far as what you might choose to block by default (so you don't have to go through the growing pains yourself if you don't want) or they could decide to whitelist instances which would then affect federation. And, as seen here, they can also defederate from any instance at any time if they feel the need.
If you're running your own instance, of course, you're the one calling the shots so you make those decisions and can federate with everything if that's what you want.