If - due to a run of warm summers - the water table didn't appear at a level in the ditch and the spoil etc. from the ditch sides started to accumulate in the bottom of the ditch, then perhaps there would be no witness marks or silt?
Yes, or an alternative scenario: there was water and silt at one stage, and later they dug the whole thing out - perhaps in an unsuccessful attempt to get down to a dropped water table? and thereby removed all evidence of silt.
Current water table levels in Avebury and Beckhampton are very very low, and likely to drop further because there was little rain last winter, but they are still well above the 1976 levels. Who knows what things were like thousands of years ago.
VBB is convinced that the secret of Silbury centres on water. Maybe the same is true of Avebury?