See inside for more info. Just a quick demonstration to show how to prevent overlapping with transparent pen. Drawing a line uses the transparent pen once, and using the pen down block draws a dot, leading to some overlap. Fortunately, switching to the desired pen color after the pen down block does not draw anything noticeable until the pen is moved.
For gtoal's question on transparent squares. https://scratch.mit.edu/projects/165603353/
