Hello c-r-o-n-o-s,
If the coordinates are not measured accurately by onboard GPS, I think you should rely on the control points only.
You may perform some calibration flights over the area with precisely measured control points and take two sets of images: at first regular flight - taking photos in-flight, then custom scenario, when drone stops to take the photo. Thus you can check, if there's any time offset between the camera shutter and GPS device. If there's any, then I think the drone requires some maintenance, as the source of the problem should be fixed.