A "good" queen (the one said to be from mite/varroa resistant stock) will be accepted by the cheaper package of bees. Within a few months she will have replaced the colony of package bees with her own "good" offspring. As long as she is laying, the colony will have her genetics. If she swarms, or is superceded, the genetics of the colony will change. A new queen will mate with drones in the area and those genetics are passed on. This would possibly water-down the genetic traits you were supposed to be getting from the more expensive queen. If you truly believe in the genetic stock you are considering, you will probably want to plan on requeening from the same source every year or two, to ensure that the stock in your yard stays true.
I'm a newbee and could quite easily be wrong, but you may be better off spending your time and money on local mutts. Maybe put one of those pricey queens in one package, and put a local mutt in the other package. Let them start as evenly as possible and see if you get your money's worth of difference for those genetics. I wonder....Maybe I'll do that.