Downloaded. Opened. Drew a rectangle. Filled with #FF0000. It spit this out: https://gist.github.com/JacksonGariety/6766626 (after struggling and realizing CMD+S wasn't saving my file) I feel sorry for whoever was tasked with making this application.
We are glad you are trying out GWD. You are correct that it seems like a bit of overhead just to render a simple rectangle. However, as alphakappa astutely observed, there is some overhead to parse the JSON data which describes the various shapes and to render those shapes in canvas(es).
What you see is the entire canvas rendering library used by GWD. That code will be reused for additional shapes you create, including more complex shapes you can create with the Pen tool.
You bring up a great point though. In most cases, you probably don't need to draw shapes (and the overhead that comes with the runtime). If you want to rectangle elements on stage, a much better option is to use the Tag tool (the fourth tool from the top) and add HTML elements such as DIV and give them background colors and modify the border styles using the Properties panel.
We are working on our help documentation to educate our users in how to optimize their content in both size and performance.
Thanks, Google Web Designer team - aka the ones tasked with making this application. ;o)