Section 6.2.4 of the PCI specification states:
These registers are used to uniquely identify the add-in card or subsystem where the PCI device resides. The provide a mechanism for add-in card vendors to distinguish their add-in cards from one another even though the add-in cards may have the same PCI controller on them (and therefore the same Vendor ID and Device ID).
Or in paraphrase they identify the PCB the IC sits on.
"... add-in card *or subsystem* ..."
I agree the spec could be more clear, and that it doesn't at all give guidance on how these IDs should be used; but it certainly does not say that completely unrelated devices should be assigned the same subsystem ID, just because they are soldered to the same board.
Segher