WP Discourse version 2.1.1 has been pushed to WordPress. It fixes the issue with the “Remove WordPress Comments Template” setting not being respected.
The logic that setting uses is that if it is enabled and a post has not been published to Discourse, the WordPress comment template will not be loaded. If the setting is enabled, and the “Show Existing WP Comments” setting is enabled, and the post has existing WordPress comments, the WordPress comments template will be loaded. This behaviour matches the setting’s description, but possibly it should be simplified so that if the “Remove WordPress Comments Template” setting is enabled, the WordPress comments template is never loaded.