The practice is very old; a tenth-century English canon describes the penitent traveling far barefoot, with fasting and prayer. The Church's present teaching holds two things together. St. Paul VI invited the faithful to accompany inner conversion with voluntary outward acts, and he rejected penance that is "purely external." So these gestures are free, personal and never a competition.
You will meet the custom well beyond those three places. Pilgrims commonly describe people crossing the great prayer area at Fátima on their knees toward the Chapel of the Apparitions, often in fulfilment of a promise, and climbers going up Croagh Patrick in Ireland barefoot on Reek Sunday. Where a custom is local, such as crossing a sanctuary on the knees to keep a promise, it is a popular devotion and not a rule of the Church. If you are simply visiting, stand back, keep the path clear and do not photograph people at close range; nobody will think less of you for walking.
Good to know before you try it: these gestures should not injure you. Anyone with diabetes, poor circulation or joint problems should take medical advice before going barefoot or kneeling on stone, and is no less a pilgrim for choosing not to. At the Holy Stairs, side staircases let those who cannot kneel reach the same chapels. Customs differ by place, so follow the shrine's own guidance.