We also spoke to Koray, Atak Translation, today and it seems that it is a software program at the Notary's that has only a space for a kimlik number therefore they cannot put in a passport number.
It was the same problem earlier in the year when you needed a kimlik number to buy a car. That was resolved so he fully expects this problem to be resolved within a few weeks and then you will be able to buy and sell a car without residency.