That's a difficult question because it depends upon several things, including the coordinate system you choose and whether or not you use GCPs with exact altitude values.
As near as I can tell the altitude values in the EXIF info for each image from a Phantom Pro 3 comes from the GPS altitude recorded during the flight and comes in as Feet Above Sea Level. Those values appear to be accurate relative to each other but can be off by hundreds of feet on any single mission. P3P units not sold in the US might be set to export the altitude values in meters, which would be much more useful.
My experience has shown that using the AGL value for each image makes much more sense, and you can get those values from the P3P flight log info. I use the Ultimate Flight App which gives me not only a repeatable and accurate altitude value but also the heading (yaw) and gimbal angle if you need it.
Converting those values all into meters and creating an import file means that everything goes into the alignment process in meters.
Since I don't use GCPs, the alignment process and all subsequent calculations and exports are done using AGL.
If GCPs were used, and you chose the export coordinate system as WGS 84, I assume the elevation values would come out as meters above sea level.
For volume calculations in my applications, as long as the elevation values are accurate and repeatable relative to each other, I'm not sure the difference between AGL and ASL matters.
A gravel pile with a given set of dimensions and geometry would have the same volume whether it was on the sea shore or in the mountains.