Root Level To Be Custom Post Type Post

This is possible, you just have to set the Hierarchy setting for that CPT to “Post Parent”. Then, as long as you have the hierarchy relationships setup (via the parent_id field for the CPT post instance), Breadcrumb NavXT will follow them. However, it has limitations, namely you must setup this hierarchy and you can’t have taxonomy terms in between the two CPTs in the breadcrumb trail.

While the “Root Page” feature isn’t meant to do this, you should be able to override it with the ID of the CPT instance you want as a root. Breadcrumb NavXT itself is quite flexible, the UI in the settings page simplifies some settings, reducing the apparent flexibility.