I get the feeling that HMPO might have a fixed set of locations for place for birth in their system. Hence, if you were born in a certain village, but that village is still part of a larger better-known city/place, HMPO may decide to use that better known location.
Honestly, I would not bother getting certificate amended. It takes a lot of time and they may ask you to pay a fee. Also, you will probably get bad advice if you call the hotline for help. If you are really fussed about getting certificate amended, I suggest you email (
Citizenship.support@gsi.gov.uk) or write a letter to home office. All the best.