In the BOM editor, if a part is changed from "Normal" to Referance" the change is made at the part level. If that change is made in the browser (RMC BOM Structure) from Default to Referance - it is an assembly level override, the part remains a "Normal" part. The BOM editor reflects the part as referance, without a way to differentiate the assembly level override from the part type change.
There should be a graphic indicator in the BOM editor showing that it's an assembly override.