I think I just discovered something. I was looking at the maps for ALttP and OoT and it occured to me: One of the maps is distorted! it's impossible to tell which one, because both use their world maps for their in-game maps. When you take this into consideration, there's absolutely no "oddities;" Hyrule castle is in the same place! Look at the maps; in both of them Hyrule castle is directly "south" of spectacle rock/death mountain. (assuming of course the arrow on the OoT map points to ALttP's north)
Actually, Hyrule Castle is quite a bit closer to Lake Hylia in aLttP than in OoT.