Probably you refer to this article on how to compute the volume difference: https://support.pix4d.com/hc/en-us/articles/202559189
If you have two projects at two different moments in time of the same area. The workflow I usually recommend is to compute the volume of the area of interest in each of them and then calculate the difference, e.g. in an Excel sheet.
If the base surface of the volume remains the same and you add or remove some volume from the pile, a trick is to export the base surface in one project and import it in the second, so that the comparison is more accurate. This will avoid clicking errors.
As for the GCPs, I think it is not an issue as long as you use GCPs in both projects. The accuracy of the reconstruction will be similar in both, as long as the GCPs are well distributed over the area and if possible close to the volume of interest.
Maybe other Community users who compare volumes regularly can share their workflow and tips too. :)