It would have been helpful to have provided all of those extra facts earlier.

Those concerns do suggest that you have raised red flags about establishing a false identity and you are being asked fairly routine questions which would be asked in a background investigation to match where you say you have lived against where the person with your name did live. Presumably those match and you get your Passport.

Those are not unusual questions and the Passport Office person certainly had to answer those same questions as part of her employment application as to tens of thousands of people seeking routine government and private sector jobs which require some form of security clearance.

As to your mother's information, while the information may not be complete, what about going back to your aunt to obtain as much as possible. Not just off the top of her head, but perhaps your aunt will recall the exact location where your mother was born and you will be able to obtain at least an abstract of her birth certificate. Your aunt may not remember every address, but many people lived in the same place for many years and perhaps that included your mother? Perhaps your aunt knows that information.

Beyond that, I would still obtain that affidavit from your aunt and have the affidavit be very clear that your mother and father are both deceased and that your aunt is your only living relative and that your aunt was physically present at your birth (which is the key point about an affidavit from your mother).