The picture isn't clear enough for me to see the problem. But try to find a substrate that dries out on the top layer, yet stays moist underneath. You can keep the substrate drier and have a moist sphagnum moss hiding place, and that will satisfy the humidity issue with your redfooted tortoise.
If you think it's shell rot, you can keep the tortoise dry for a bit and smear some athlete's foot cream on the spots and see if that helps it any.