From what I can tell the new Assembly Costing Functionality does not consider Sub-assemblies. It flattens everything and only sees the Parts.
I have modeled a trolley at the Assembly level. I've downloaded and added to it some Castor assemblies from 3D Content Central. So these are sub-assemblies. I've assigned a "Purchased Cost" custom property to these Sub-Assemblies.
My hope was that when I run Costing. It would see the sub-assembly, see the top level "Purchased Cost" custom property and use that rather than try and analyse the Parts within the Castor sub-assembly.
I understand that I could convert the sub-assembly to a multi-body Part to get round the problem. But that is a restrictive workaround. For example I would not be able to make it flexible anymore.
I can see this being a common problem.