I would like to calibrate the the Azure Kinect I am using in iPiSoft with an external RGB camera, so I can superimpose the 2D projection of the skeleton into the RGB image of the external camera.

What is the center of coordinates that iPi Mocap Studio uses for the camera? Is it the IR camera or the RGB camera?

Center of coordinates you see in Mocap Studio is an arbitrary point on the floor surface, somewhere in the assumed capture area. You can see coordinates of an active camera (as well as its view target and rotation angles) in this coordinate system on the Scene tab. There you can also save those parameters for all cameras into an .ipiscene file which is a straightforward XML-based format. Position and view direction of a depth camera is defined by its depth (IR) sensor.