Think you'll find, ST, that the final stage of Silbury was constructed of chalk, not just had a chalk covering. A clay covering of the foundations (above any seasonal waterline the structure may have been subjected to) would make perfect sense for any phase of Silbury.

Silbury, when finally completed, would have appeared as a brilliant white structure set in the valley between the Winterbourne and the Kennet. The builders must have known that left like that it wouldn't have lasted very long - weathering from the elements above and flood erosion from below. So, after millions of man-hours to build Silbury, how would the builders have gone about protecting it? Clay at its base perhaps and the rest covered with turf?