The system appears to have sacrificed itself for the happy ending despite knowing it would be sent for 'repairs' as punishment for violating system guidelines. The exact repair method is not elaborated on, but other system novels would indicate that the worst case scenario would be essentially death: complete wipe and reboot. Best case scenario they only fix what may be defined as broken. Emotions are a feature not a bug, so system may be OK. The term punishment means that the process is somewhat unpleasant regardless.

1. The Villain is the Greatest Assist - I did not expect the villain to be an ally at all. I was waiting for the mansion to turn into a bloodbath even after the protagonist began to trust the villain. Perhaps even a major betrayal scene. None of this. I was also disappointed that we never saw him again even as a guest at their wedding.
2. The ML is truly a book character - Usually ML's have an existing real world identity. A comment about choosing a 'partner' in the first few chapters also made me think they entered the world together so I even suspected that the ML was his older non blood related brother. The partner being paired up was probably the system being allocated to the host and I misunderstood. The system finds a way for the main characters to have the perfect ending despite the ML being a real paper person. Most of the extras are the MC trying to adapt to life without ML and then trying to help his family adapt once he appears.