The shifted landmasses was for realism, because the current iteration of this bigger map seemed to distort the northern coast of France by making it too steeply diagonal. Shifting France and Iberia up makes the northern coast of France look more realistic IMHO, and the Britain shifting is done both to accommodate that and because Britain seemed too far west to me.
Did you like my proposal for how to make Italy look and play better? (Shifting Sardinia and Corsica 1S so they aren't connected to the mainland or each other and an extra land tile west of Rome)
As far as Koenigsberg, since it was apparently built on the river, either side is equally correct, and putting it north reduces the crowding with Danzig, Warsaw, and Vilna. And although it is crowded, I really think that Koenigsberg is worth including, as is Brussels. Having both Koenigsberg and Danzig will help create more competition for ports between Poland and Germany, and make the Baltic more interesting in general.