The most restrictive status takes priority, it doesn't matter if it is a system or user status. If a user status allows something and a system status forbids it the process is forbidden. You can look in the status information and see what status is preventing a business process.
If your users wants to change planning after TECO it is a simple matter to revoke TECO, change planning, then reset TECO. Why the plan has to equal the actual is another question entirely.
That's why core mods are taken at your own risk, it all depends on what is included in the support pack on what is updated.