A message will be attached to the message to which it's replying, whether or not it appears in chronological order. Often you'll see only one message per HTML page. The result is more like a real conversation. Often with a linear system you can read more than one post per HTML page, which speeds things up when you're reading. Once you have your community goals worked out, your users in mind, and your tools selected, you have a good foundation for community building.
Any community needs host tools.
You'll sometimes have the ability to edit or hide or delete the posts of your members, or to move those posts to a more appropriate area. Host tools allow you to do all this, and sometimes more. Occasionally it's necessary for you as a host to step in and revoke the privileges of that user to post. Or to moderate their posts - meaning that you will review what they have to say before it's made public. Sometimes in a chat situation someone needs to be removed forcibly from a room and kept out.