The third source point and destination point are used to specify direction, take the following of a rectangle and a splash as an example, as shown in the following picture,

Executing Align command and specifying the first two source points and destination points, then it’s time for third point and the rectangular will be located to a different place, as shown in the following picture,

If we specify the third destination point below the splash line, the rectangle would be in the different direction, as shown in the following picture,