I see what you want, but it's going to be rough going getting it.
For example, if this was a rivnut, you'd have no problems because it would work the way you want. It is impossible for it to both be altered and unaltered at the same time for the BOM and part drawing.
If the BOM is really desirable, then I'd look to making a little plug part that represents the boss you want and is then filtered out of the BOM. The little part would be seen in PDM as a part, but with a name like "Pierceandtap" so no one orders it.
Inheritance is an alternative that provides the 'make-from' traceability, but not the BOM support.
It's unlikely PTC will do anything about this, considering that the same case applies to creating weldments, for which they did not create a general-purpose solution to adding material in assemblies. Similarly conformal coating, plastisol dip, and various forms of encapsulation and potting. It will take AutoDesk or Siemens or Dassault Systèmes to sell a product that does this -and- start taking away a lot of PTC sales. THEN marketing will get the software developers to catch up.