Assuming that the stud was screwed in from the top, stud removal tools may mark the thread, especially if the stud is tight / corroded into place. But, if the stud is never going to be re used, damage should not matter, as long as it comes out without shearing off.
If it does, you are in the "centre, drill and tap" routine, so you need to certain of the thread (Looks like BSW to me? )
Howard.