We will be in next 2-3 years... (if they ever let me proceed with the upgrade) we try to separate as designed software wtpart and with or without mpmlink, go the as designed route such that the chip or device in the product or sub assembly holding the software is the as-built mbom.
Integrity integration in 10.1 with the software module let's you take those software parts and tie them to the software builds and releases stored in Integrity or other versioning tool like clearcase or subversion...
Important thing to note: the software instructions might be the same in design, but used differently as constants or properties/attributes on the mbom.
Good thing also is this gives you ability to associate specific work instructions for the manufacturing user, engineer, supply/procurement, or process planner.
Not sure if this is what you were seeking, but figured can't hurt to share.
Sent from my Verizon Wireless BlackBerry