Hi @jacob-presley, good questions.
Yes. The rooms can have different heights when there are different roofs above them and there are no other rooms on top. In case there is a room between the two, then you need to split the roof. @chriswmackey and I have discussed potentially automating the step of splitting the roofs, but it hasn’t been on top of the list.
The assignment of roofs can be changed manually in the upcoming version of the Model Editor. The rooms will always be mapped to the roofs that are associated with that level.
Here is a short recording that shows how to work the segment that you highlighted above.
Let me know how it goes, and if you have any other questions.
P.S. If I were you, I would export this model level by level, and make sure everything is correct with the rooms before dealing with the roofs. That would have given you a much better starting point.