Adding GCPs does not affect the shape of the processed elevation model and since making the volume measurement is a relative measurement they don't matter and shouldn't be used.
Our GCP system was designed for non-geotagged images as a way to georeference the outputs. If your camera already has tagged images you should not be using the manual GCP system.
If the barometric altimeter was having issues it is likely your aircraft would not be flying very well since that is the main altitude sensor.
There have been changes to the way the data is being processed on our side.
In general, if you really care about your 3D model quality or elevation data accuracy it is important to use plenty (80%+) of overlap in order to make sure the system has enough data to process things accurately.