If you use the WP Discourse plugin’s default settings it will give you the first 5 replies in sequential order. The plugin should probably have an explicit setting for this. The limit on the number of replies is set by the Max Visible Comments setting. You can set the Max Visible Comments to a very large number. It’s possible to write some custom code to paginate the comments - I did that a while ago. I have it somewhere on GitHub and can look for it if you’re interested. I think a better approach for when sequential replies are being used would be to display the first batch of replies and then have a Load More Comments button. Clicking that button would pull more comments from Discourse and load them on the page.
Adding a comment box window isn’t difficult. The post’s Discourse topic id is added as post metadata with the key discourse_topic_id. You can create a post for the topic through the Discourse API. The reason for not including this in the plugin is that we’re trying to move the commenting to Discourse as a way of improving conversation. There may be legitimate use cases for allowing people to post comments directly on WordPress.