Hi Will,
Currently, Pix4Dmapper can only export outputs in a projected coordinate system. This means that if your input coordinates are in Latitude, Longitude, Altitude, your outputs’ coordinates will only be in meters or feet, depending on the selected output projected coordinate system.
You could use an external software to do the conversion (any GIS software)
I will transfer your need as a suggestion for improvement. Our Product Development Team will consider it for future version of the software 