What are the documents required to ensure
A) Builder honors his commitment and our interest is protected
the development agreement in original containing the agreed terms;
B) The title of the new flat is clear so that my mother can sell/transfer/gift/WILL/lease it as and when she desires.
Once the developed property is allotted to your mother on her name, she becomes the absolute owner having full rights over the property for all transactions at her disposal.
C) Are there any documents that need to be registered?
The subsequent document on your mother's name to be registered otherwise it will remain invalid.
Beter consult a local lawyer and get his furthe advise on the subject.