Note: there is never a water tile next to the start board and end board.

In my opinion there can be a water tile next to the start board or end board.
The rules just state that when there is a hole next to the start/end board then this hole is not filled with a water tile but the board is moved towards the first/last tile.
Now, if this first/last tile is a water tile it creates a situation where there is a water tile next to the start/end board.

If a gap appears at the beginning or at the end of the path, move the Atlantis tile or the mainland tile so that the gap is eliminated.

I don't know where you quote comes from, but the English rules on Amigo's website state the following:

Spaces containing water tiles are still "gaps," so you would simply remove the water tiles "so that the gap is eliminated."