I think that they are calling the underworld an in between place simply because then they can have some characters there and not others. I think it is as simple as that.
I completely agree with wickedregal’s thought about the flower. That was exactly what i thought. That Hades is upset because there is life in the Underworld and that is why he is going after the group. Maybe he has collected these souls and Emma and the rest help some of them move on.
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