As the other person mentioned, it matters to an extent because the admins of your instance have the ability to cut ties with other instances (defederation). They also have the ability to make instance wide actions like banning a community belonging to that instance (in the same way Reddit admins can ban a subreddit).

Some instances will naturally be stricter about what types of communities are allowed and what types of instances they will federate with. For that reason, it’s important the instance you join aligns with your values, e.g. you probably don’t want to join an instance that tolerates alt right communities.

Comments and posts sync. We are on different instances but are still talking to each other.

Just think of each separate site (AKA ‘instances’, like lemmy.world, sh.it.just.works) as different competing versions of Reddit. All with their own different subreddits.

The key difference though is that these instances are all partnered together (‘federated’) because they are running on the same technology so you can see posts from the other instances.