When you write that it is a "Y Fare" do you mean a ticket in the coach cabin or in the Y fare bucket? If it is the latter, you'll get full credit either way. Either way, it has to do with the fact that CO chooses what price to charge on the flights sold with the CO code on them, and they will often charge much more for codeshare flights than the operating carrier will charge and/or will limit the fare buckets that they will sell. In this case it appears that CO is only willing to sell you a true "Y" fare because of the codeshare (Y2R or Y2SGW), while NW seems to have a much lower published Y fare (YKE) on the route. Given that, just buy the NW fare.