I had the same issue in a tool script with a setter and found a proposal with a discussion of this problem. I used this workaround for Godot 4 from the discussion. Your get/set function would become:
@export var color: Color:
get:
return polygon2D.color
set(new_color):
if not is_node_ready():
await ready
polygon2D.color = new_color
Seems to work here, there’s no error anymore when loading the scene. The error before was: Invalid set index ‘color’ (on base: ‘Nil’) with value of type ‘Color’.