If a another plugin is used it would make it difficult to have the custom post look and behave like standard posts. Atelier already lets you choose a custom post type for both the blog and recent posts page builder element, it just makes sense to be able to change how the posts are filtered.
As for implementation I would suggest under “Advanced Options” just below “POST TYPE OVERRIDE” that another pull down with “TAXONOMY OVERRIDE” be added.
I would appreciate if you would pass this on to the developer so he could evaluate how difficult this would be to implement.
I use custom post types often in my work and most themes are not much help with this. Atelier is just one small step away from making this easy.
-Ian