As far as I know, these Gcodetools extensions don't have such an option. However, I'm not intimately familiar with them. It's possible there's something for that, and I've just never seen it.
However, if you didn't use Tools Library, you didn't use it properly. I think there's a chance that setting the correct tool and width, using Tools Library, might fix both problems. It probably will fix the problem with the rectangles, and then you don't have to make any correction. I'm not sure if it will fix the problem with the circles, but it might. Unfortunately, since I don't have any cutters, I can't really test it myself.
Try setting the tools, using the extensions in the order I explained above, and see what happens. If that doesn't fix both problems, let us know, and we can investigate further.
If it doesn't fix the circle problem, please share your SVG file with us.