JALSnipe - under the impression if buying a mutli-airline ticket under one carrier - all component airlines have an interline luggage agreement with the purchasing airline. Looking at the ticket again - So the flights are not codeshared (ie UAxxxx flight numbers), but would have interlining luggage transfers. I would think we would be checking in at the United Counter for "Alaska Skywest" - possibly formerly "United Express". I've never seen a United agent try to levy a Alaska baggage fee at an United help counter.