Adding to this, I was able to find out the class that sets the Values in SPRO > SAP Netweaver -> General Settings->Set Geocoding->Register Geocoding Program in the system.
Basically I created a Z of CL_GEOCODER_SAP0 and put my code in the GEOCODE_ONE_ADDRESS method, modifying the Latitude and Longitude values.
The issue I am facing here is that the altered values are stored the first time I Save an account, but if I alter the values next time, the values are not updated.