While there's no need to manually cross-post anything anymore, you can choose who sees your post. You can make your post public, visible to both Facebook and Messenger friends or visible to Facebook friends only. If none of those sounds ideal, you can either make a custom list or hide Stories from specific people on both platforms.
By combining the features, Facebook is likely hoping to entice more people to use the ephemeral offering. Having separate versions for Facebook and Messenger made no sense anyway and might be one of the reasons why they're nowhere near as successful as their counterpart on Instagram. Just a month ago, the company started testing a useful tool that allows you to cross-post Stories from Instagram to Facebook. Its addition could make things even simpler, but as with any experimental Facebook feature, it might or might not see a wider release.
To make sure the new version of Stories reaches as many potential users as possible, it will be available to Groups, Events and Pages. However, Stories from those spots won't be available in Messenger. Facebook is also bring it to FB Lite in case its users do have enough bandwidth to view their friends' posts.
Update: This post has been updated to clarify Stories from Groups, Events and Pages will not be available in Messenger.