Union deaths amount to ~665,000. Confederate deaths amount to ~485,000. This seems very strange to me knowing that:
Well, for starters, your numbers are wrong - you're counting all casualties as deaths. The appropriate numbers are more like 360,000 Federals and 289,000 Confederates, the rest of the casualties are wounded or captured. Of those, 110,000 Federals and 94,000 Confederates were killed in action or mortally wounded.
About 225,000 Federals and 164,000 Confederates died of disease. This is where the advantages of the North in taking care of their soldiers showed, because that was a 10.5% of the 2,100,000 Federals and 15% of the 1,080,000 Confederates. Death from disease is not generally going to have any connection to the resources available to your enemies.
So in the end, about 17% more Federals died in or due to combat than Confederates. The cause of that is likely because of the nature of the war. Although there were notable Confederate invasions of the North, and notable battles where the Confederates utilized a tactical offensive while on a strategic defensive (Chancellorsville, The Seven Days Battles), for the most part the course of the war involved Federals attacking Confederates holding a prepared defensive position, putting the Federal soldiers in a more exposed position in the fighting, resulting in more soldiers dying.