The Evaluation documents indicate that the ancient city area IS included in the inscribed area even though it is not given a separate section as are the buildings with "pretty tiles"! It is specifically mentioned on several occasions however eg
"Afrosiab is the ancient site of the town before the Timurid period dating from the 7th century BCE to the beginning of the 13th century CE. It has the form of a triangle and an extent of about 289ha. Archaeological excavations have revealed the ancient citadel and fortifications, the palace of the ruler, and residential and craft quarters."
And elsewhere "The ancient city of Afrosiab has preserved its original forms and unique wall decorations, which are now conserved"
I understand that Marakanda occupied this area :- "At the time of his arrival, Maracanda was the capital of Sogdiana, occupying the hill of Afrosiab that rises to the north of the modern city".
We could also have an "Assassination" connection for Samarkand as Alexander murdered his general Cleitus during a quarrel whilst they were at Marakanda - if you don't think that is stretching the word "assassination" too far.