So, I found it. It seems to be a feature, whereby I cannot imagine any kind of workflow where the resulting IFC is correct: the issue above happens when in the IFC Translator > Data Conversion > IFC Space Containment is on:
Hello Lazlo, it might be, nevertheless the behaviour is curious to say the least and it doesn't lead to the expected IFC structure.
I did observe that if even the tiniest intersection between a room and a wall would cause the room to embed the wall. So we had, for example, a parapet wall from the floor above listing into the floor below (and in the room), unregarded the floor assignment.
The floor assignment should take priority.
All openings in the involved walls also move into the room, this is probably due to the nature of Archicad. But please tell me how that makes sense, when the openings of a wall in another room or floor list into a room.
Basically, I gather that this feature is meant to offer a visual alternative to IFC relationships, but the solution is far from optimal. I would strongly suggest to warn clearly the users upon click.