On PTGui's example/tutorial page http://www.ptgui.com/examples/, it has a tutorial for how to add a handheld nadir image to a panorama, using the viewpoint correction feature of PTGui Pro. However, what if I want to do a HDR pano. Can I do handheld bracketed shots of the nadir? How can I stitch these nadir images? Not to mention I must erase my foot from the nadir image.
Assuming you are using a tripod for all the other shots, why don't you keep the camera on the tripod for the nadir as well? There is then no problem with bracketing. All you need do is shift the tripod sideways and point the camera at the original nadir, or lean the tripod over as described in http://www.rosaurophotography.com/html/technical6.html.
Excluding feet and tripod legs can be accomplished by applying an alpha channel mask (see http://www.johnhpanos.com/alphatut.htm), or by adjusting the blend priority on the Image Parameters tab.