Currently, the AA is preventing the fragment shader from running again on shapes below the edge of the shape receiving AA as can be seen below. This is creating a dark circle around the edges of each shape. I don't know the reason for this happening.
Turns out the issue wasn't solved and AA is still causing outlines when shapes overlap. This appears to be an issue with the alpha blending for reasons I haven't figured out yet.
Currently, the AA is preventing the fragment shader from running again on shapes below the edge of the shape receiving AA as can be seen below. This is creating a dark circle around the edges of each shape. I don't know the reason for this happening.