I'm not sure what instigated the thread, nor how your currently managing BoMs, but I can share we have steadily worked to seperate the definition of Engineering "requirements" (in Windchill) from the Operational execution "decisions" (in SAP). We believe this approach scales well and supports everyones "needs".
The Eng requirements are defined "Make vs Buy agnostic". Meaning the requirements do not define sourcing and are the same regardless of source. The exception is when a specific supply chain is required due to something proprietary.
The Assy has no requirements and is only for modularity.
In the Purchased Assy example:
If multiple supply chains, and one includes inhouse assembly, the components would not be phantomed in MRP.