I just solved this after getting some ideas from this thread. I agree though, it should be much more straight forward - crop and zoom to cropped area.
Zoom on the area you want to keep for the final clip (obviously!)
Using the original clip resolution, apply the percentage zoom you selected for each dimension to the pixels i.e. if your original clip is 1280x720 and you're wanting a cropped video of say 45%,0%,90%,100%, then the start pixel of the horizontal is 45% x 1280 and the end pixel of the horizontal is 90% x 1280. That puts your crop in the horizontal position between pixels 576 and 1152.
Export the clip with the final pixel sizes as determined by your crop percentages and calculations with the restraint ('Widescreen fit' in the export dialogue box) to STRETCH. In this example that's 1152-576=576 for the horizontal and 720 for the vertical. But remember that the top left pixel is 0,0, not the bottom left.
