Yes, it’s by design: you can not revoke a capability from administrator role, you can just add a capability to it.
Is it critical for your purpose to have option “Force custom post types to use own capabilities” turned ON? If not, switch it OFF at URE’s settings page and you will get access to this plugin back.
We met the incompatibility issue here.
I suppose that “Booked” plugin defines booked_appointments custom post type capability mapping some special way. I need more time to find a workaround…