Thanks for your quick reply! It is common to see more discrepancies in your volume calculations without the addition of Ground Control Points. That is expected given the relative accuracy of your drone's GPS.
I also think an explanation of how we calculate volume might be helpful here. We add up all the individual pixel volumes to calculate the total volume. In doing so, the uncertainty in your volume estimate is basically a function of how small the pixels are (resolution), and the uncertainty of each pixel height reconstructed by photogrammetry. Additionally, the world isn't perfectly flat. Since there may be a slight incline to the area in question, we have to subtract out the height of the "base plane" from the elevation value at each pixel. We do this by choosing a 3d plane that best represents the ground at the perimeter (an average), and subtracting that plane from each pixel height. This is likely the reason why you are seeing slight inconsistencies.
I hope this additional context makes sense! In terms of best practices, you definitely do want to be careful about placing the points evenly throughout the stockpile. This should help with accuracy.