At my day job, we have an ERP system which uses house part numbers which map to orderable part numbers. That's the application you reference. Engineering only cares about the house part numbers, in the sense that they are embedded in the schematic components.
In other words. I don't particularly care whether we buy Panasonic or Yageo or Vishay or Susumu 1% 0603 resistors. The house part number isolates engineering from those purchasing issues. This is all above the level of the schematic and PCB.
Certainly when parts go obsolete, purchasing asks engineering whether suggested replacements can actually work in current designs. If they can, then in the ERP system the new manufacturer part numbers replace the obsolete numbers.
If there is no form/fit/functional replacement for an obsolete, we remove it from the company library and it gets marked as such in the ERP system. This means that it can't be used for new designs. The bosses also make projections about how many boards which use those obsolete parts will be built in some given time frame and we'll do last-time buys to meet that demand. Those boards also get flagged for future updating to replace obsolete parts.
That's all beyond the purview of a CAD program!
What about when you use multiple suppliers? I know our purchasing person trades off between all of the usual suspects when ordering, so she needs to start with a manufacturer's part number, not the supplier's number.
I realize that hobbyists don't care about this, but the goal is to encourage the use of Kicad in professional environments, and I suppose that's why there is so much discussion about BOMs.