This is done for several reasons.
(1) Logos of some tannery on a brand new sole are ugly.
(2) The soles or heels that are used can be old, and a bit dry, especially if they're kept in an arid closet in the back of the shop. A cream/moisturizer is applied liberally to the leather, and seeps in, conditioning the leather and thereby making it more durable, more flexible, especially in cold weather.
(3)It allows a new finish to be put on, polished and shaded to blend in well with the rest of the sole.
Yes, we actually are that anal.