>For instance, the Avebury stones can't be in exactly the same place, just because they found where the original holes were, can they?

Yes they can.
When the stones are packed into the hole they settle and create a mould around the bottom of the stone in the chalk.
Stone holes excavated on the beckhampton avenue since 1999 show a definate shape to the remaining side and the stone can be accuratley matched to the hole.