It would be neat if you could adjust the suggested rectangle or polygon, rather than rejecting the image or drawing a rectangle/polygon from scratch.
Do you at least have an idea or a suggestion of how to approach this problem? Any response would be appreciated.
If you just want to adjust the position of a shape, you can already use the arrow keys to move it by one pixel in either direction.
If you want to change the shape itself, you currently have to redraw it. For rects, that shouldn't really be less efficient than dragging individual corners. For polygons, that's a bit trickier and I haven't really found a good solution that's easy and efficient and ideally also supports keyboard shortcuts. That feature request also hasn't come up much before, but if people are interested, I can look into it again 
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I'm also very interested in this. In my situation it would be much faster to edit the rect height/width only rather than redraw.
Just released Prodigy v1.10, which includes the new and revamped manual image UI that supports moving and resizing bounding boxes!