I spoke with matt today. Our recommended approach for aligning to an edge is to cut the board after printing and baking (if you can). A quick cut with the right tool will be faster in some cases.
Alternatively, you could do an aligned print using the top and bottom pads of the usb connector. You'll need to click one of them during the first "Move To Pad", and the other during the second. Note: the first pad is used as a pivot point and the second determines the rotation of the board around that pivot. Generally we try to keep the alignment pads far apart to minimize the impact of measurement inaccuracies, but you should be ok here.
As you suggested the outline is just a rectangle with some padding. I've made a note to fix a bug there: the box we draw around the circuit does not match the path that the probe traces...that was intended at the time (they are different things), but if i made them the same that would be more useful and clearer.
I noticed this too if you pinch the clamps for maximum coverage. I was told that the clamps don't need to be in that far. They're to keep the board from wobbling so you don't need much contact.
Let us know if this will help,