Yes this is a problem we have come across. A lot of our workflows start with Revit for massing and other geometry creation, so Revit seems best placed to generate the boundaries and spaces for BEM. However we have been unable to extract the correct IfcRelSpaceBoundary derived type from Revit IFC export as of yet.
It may be possible through some form of Revit IFC export customisation, but I am personally yet to see it actually spit out an IfcRelSpaceBoundary1stLevel or IfcRelSpaceBoundary2ndLevel object type. It does indicate the boundary level in the description, but inner boundary information would be absent for level 1 boundaries, and adjacency information would be absent for level 2 boundaries as these are attributes of the derived object types and not IfcRelSpaceBoundary.