First of all, a
Area2D both don't have a size. What you perceive as size is either the sprite or the collision shape they have.
They don't align because your collision shape is centered but the child of your other Node2D is not.
I see two ways to center tour area:
1) When you assign the position of the area, add an offset equal to half the size of your area, half the size of the target node2d, or an average of both if their size differ
2) Design your game objects such as their root is centered instead of being top-left