This issue demonstrates a bug I'm seeing when rendering WebGL with Swiftshader in headless mode.
On Linux (Tested on Cent OS 7) run these two commands
node screenshot.js --headless=true
xvfb-run --server-args='-screen 0 1500x1500x16' node screenshot.js --headless=false
When Chrome is run in headless mode (headless.png) the transparent regions of the overlayed image are visible.
When using XVFB to run Chrome (xvfb.png) you will see the underlying color in the transparent regions.