So, I'm not sure if the export window is a temporary thing, or what... But I'm finding it very clunky and unintuitive. I have more details and screenshots at the end of my blog post, but basically, I would suggest, if possible, to merge the export window with the actual canvas so that you can toggle the bounding box at any time while editing, and change the size of the bounding box using the same kind of transform controls as the sprite transform controls (minus rotation, of course).
I'm using the beta that you have linked on your site, so I'm not sure if there's a more updated version that's better than this...
Other than the exporter, I really like this product!