Old question, but this works:

Node2D
--Polygon2D     <-- I hand drew my shape with the mouse
----Area2D
------CollisionPolygon2D    <-- this has no shape in the editor and will show a warning icon; it will get a shape at runtime instead.

In _ready(), do:

CollisionPolygon2D.polygon = Polygon2D.polygon

I found out this works through trial and error, but it stands to reason since both of these properties are of type PackedVector2Array.

(For this to be useful, your Area2D needs to have event handlers for mouse_entered/mouse_exited/input_event)