Marking this as resolved. There must be another plugin causing this problem. I installed and tested in a sandbox with just CPT UI, Post Type Switcher, and Remove CPT Base and everything worked as expected.
I have installed your plugin and it works great with my custom post type when I create a new post, however, when I use the Custom Post Type Switcher plugin to change post to my CPT the /cpt/ base gets removed but the URL yields a 404 error. It’s interesting that URL of the original post is the same as CPT after using the switcher. I would think that URL would still work.
The paths look like this for the original post type:
And like this for the custom post that I switch to:
But, I still get 404s. Even after turning on “alteration”.
Are you aware of a conflict with these two plugins? Is there a workaround?