Even if all the individual wires terminate in connectors and the connectors are unique and cannot be mixed, there will come a day in the life of the product where someone needs to troubleshoot a circuit or repair wire(s) in a cable. That is typically done by noting wire colors in a circuit diagram. It is not practical to trace every conductor with a continuity meter. Depending on what markets your product is sold in, there may be statutory requirements for a manufacturer to provide after-delivery service support.
If your one rogue supplier feels unrestrained to substitute different wire colors, do they likewise feel free to substitute different wire gages or different insulation materials or RoHS-banned substances in connector hardware? The manufacturer could find themselves in a legal nightmare someday if you do not maintain design control over your suppliers.
