In the original version of the game, new Vikings started their game by missing one such boat in the quest The New Student. While that part of the game has since been removed, players can still use the boats to travel directly between Berk and the School without having to use the World Map or the game's fast travel option. Using the Boat to travel to either Berk or to The School would remove 10 Energy Points from the active Dragon, this was been removed since.
The boat found at the the Lookout can't be used to travel in this manner.
Eret's Boat in the Training Grounds takes you to two different places (mission-exclusive):