I'm guessing they switched away from YKK zippers for financial reasons. Looking at both zippers, the Filson zippers appear to be more copper colored while the YKK zippers appear to be more yellow colored. I think I prefer the look of the YKK.
On a different note, I recently treated the bridle leather of my 246 with Obenauf's LP. The issue is that some of the stitching has turned white. Can I assume that this will eventually be absorbed by the leather and fade away? It's been three days now and there is still significant white coloring on some of the stitching.