The shell does look a little imperfect as shells go.. But you've had the tortoise for 3 years and it seems fine?... I Probably would not worry too much.
That picture was my original build..I have since modified it after researching info on keeping the humidity up.
Adding sphagmum moss as and underlayment and closing the top of the enclosure with glass keeps the humidity at 80-85%. It was a rough time fighting to keep it up, but now, I have a...