
Sometimes the consumer grade GPS gets a good fix, sometimes it doesn't. The spec is within 10 meters. Sometimes it is way less than that and sometimes it is right on. This is why we offer the realignment process.
Using 80% overlap and following the Data Collection guidelines carefully goes a long way.
The Ground Reference image is taken so we can use the barometric altimeter readings instead of the GPS derived elevation. It doesn't change the model but it makes the elevation values more accurate.
You can read more about that here:
https://support.dronesmadeeasy.com/hc/en-us/articles/206208583-Ground-Reference-Images
You have a bit too much overlap. The black areas in your Overlap Report represent places with over 50X coverage. That is too much and is why it took longer to process than usual. The recommendation is 25-30X coverage unless there is a specific need for more.