A possible - albeit much more recent - analogy might be the building of a medieval church or cathedral. Building starts in 1100 using available technology - thick walls, rounded arches and the building is planned on that basis. Then, 50 years later, technology improves and so the next part is built using higher, pointed arches, and then flying buttresses allow the weight to be distributed more cleverly, glass technology improves as well and and thinner framed, larger windows let in more light. Perhaps a spire is added. Each stage is planned - to completion of the whole buidling, not just to the completion of one corner. But the design changes, often before build, as technology advances or perhaps more money becomes available (for instance because your church is in area where the wool trade has taken off). None of it means that the original plan wasn't complete in its own right, just that things changed. That would seem a plausible supposition for Silbury, regardless of whether it can be definitively "proven".