It turns out that Pods handles this exactly as you would expect.
It doesn’t differentiate between completely new post types and extending post types in the Pods API.
To check if the WP_User
class is being extended by pods, the method is identical:
// pods() returns false if there's no extended class for `user`
if ( !pods('user') ) {
// Do things if there's no extended User set up in Pods
}