What tools and workflows are people using to manage component level electrical engineering PCB BOMs in conjuntion with EPDM?

In theory, EPDM can manage any kinds of files and any types of parts, but it doesn't seem to be a good fit for EE BOMs. We use Altium and other tools, and also work with clients who use all sorts of schematic capture and layout tools. EE BOMs have reference designators which are missing as a concept from EPDM. EE BOMs usually have allowable substitutions for common components.

I realize that companies use all kinds of systems for the ERP aspects of ordering and tracking components, but what do design and engineering teams use to manage EE BOMs during development?

I've used Arena in the past, and I know it handles EE stuff, and integrates disparate teams well, but I haven't used it in a way that is directly connected to EPDM/SolidWorks.