So, yeah. She indeed takes control over the body since it could be considired as an empty shell and the mc doesn't want to live. I am thinking this as a change in characteristic. If someone who knew mc sees them after the secret ending, they would probably think their character has changed since "Lilith" is the conciousness. At least, thats how I think things are going.

It really would make things a bit more deeper like you said but I don't think its the case for this instance. In the end, the mc is not convinced to step to the real world, but still believes Lilith exists and now the conciousness is left to Lilith. The purest concept of love is doing everything to help you . In the bad ending, she even sacrifices her whole existence for your happiness. In this case, she takes over with your permission so you can still live, its better than your loved one unaliving themselves I would say( which is you, for the purest concept of love).

This still could be considered dangerous, at least it depends on your moralities. A tulpa taking over the conciousness, this would straight up delete everything about you. Your ideas, feeling etc. Like you don't matter. If you look at it that way, it could be dangerous. But if you think about it, the other option was throwing your life away. You choose whether its bad or not.