Since I don't think it has been answered yet, the 500mb height is a function of the surface pressure and thickness (which is proportional to temperature averaged over the layer). So, BN heights can be the result of BN temperatures from the sfc to 500mb, BN surface pressure, or some combination. When the 500mb height is BN but sfc is AN, that tells me the sfc pressures are low and/or the sfc temp is higher than would be expected for a given thickness. This makes sense since Pacific maritime air masses have steeper lapse rates (warm sfc, cold aloft) than continental/arctic origin air (cold sfc, cold aloft). Think about it - air coming from the Pacific more or less assumes the SST after many days. There isn't enough time when these travel over North America to cool radiatively at the sfc. Also, the latent heat added from orographic precip over the Rockies actually results in a warming of these air masses (chinook effect). Contrast that with Arctic air masses - the cooling is strongest at the surface (surface radiates heat much more effectively than atmosphere), so these tend to have a strong inversion. Further, when you get an EPO ridge the cold air doesn't have to cross the Rockies, it comes down the eastern slope from the north so no latent heat gets added (not that there would be much considering how dry these air masses are).
Models are really good at moving air around - I'm not sure how well they represent the radiative heating/cooling though. It's pretty complex and depends on the surface properties, water vapor, etc. I remember reading a paper about the formation of deep cold air masses, and the authors found that you get "diamond dust" ice crystals - basically very light snow w/o clouds - forming below -40C (or something really cold), and these radiate heat more effectively than the air itself. At really long lead times if these processes are not represented properly it could result in a odd looking temperature for a given flow pattern. There are modeling experts on this forum who know way more than me (I'm from more of a radar/remote sensing background) , so I'm happy to be corrected.