Actually, Aonuma already explained it. Miyamoto never cared for a timeline so there wasn't an explicit one until Aonuma came on board with Majora's Mask and set one in stone. By that point in time there wasn't much debate on a timeline because there were only about 5 or 6 games and they all fit together based on their own acknowledgements (OoT -> MM ---> LttP-> LA ---> LoZ -> AoL), it wasn't until Wind Waker that stuff got bizarre and the split timeline was officially born out of OoT. So nothing is "shoehorned" because the timeline existed before most of the Zelda games that are out now. Aonuma also explained that they tend to make the games, their worlds, storylines, etc., THEN place them into the timeline afterwards. That would explain some discrepencies because a chain-linked continuity is not exactly their priority.
Tag - "No trolling on my watch!"
