As an optimization, Cobalt does not clear its framebuffer each frame, however this can indeed cause a problem if you would like to use it as an overlay.
In cobalt/renderer/pipeline.cc, right after the line:
rasterizer::Rasterizer::Options rasterizer_options;
but before the line:
rasterizer_->Submit(results.animated, render_target, rasterizer_options);
If you add:
rasterizer_options.flags = rasterizer::Rasterizer::kSubmitFlags_Clear;
Cobalt will clear each frame to be fully transparent before rendering the contents.
We will look into adding a nicer way to express this desire in the future, but hopefully this helps for now.