I found a more recent build from https://blenderbim.org/docs-python/ifcconvert/installation.html and that's working fine.
I guess I need to build it from source then. Version 0.5.0 preview2 for Windows from https://ifcopenshell.sourceforge.net/ifcconvert.html doesn't seem to have that option. When I try to use it, it's giving error "[Error] Unknown option '--use-element-hierarchy'" and option is not listed in the help page either. I'm sure it was still there few months ago though.
It seems like --use-element-hierarchy option has disappeared from IfcConvert. Are there any alternatives for this?