Madoka bites her lip for a moment. She wants to say that moreso than being safe and taking care of herself, she just wishes Nell could be happy.

But it feels a little bit too cruel to say that, especially when there is absolutely nothing Madoka can do to help the other once she leaves the train - and Madoka is well aware of that.

So instead she just politely bows to the other.

"Then.. Please take care going back home. I hope you'll arrive back there safely.. And goodbye."

Maybe all she can do is to just hope for the best for Nell.