PTgui does a nice job of stitching a flat nadir view into a panorama using viewpoint correction, provided the surface is fairly flat. Aircraft cockpits seldom have a flat deck and represent a special challenge. In fact, a tripod will not fit in many cockpits - there are few good resting spots for the three legs.
Others may be interested in the technique being developed by the author. A Manfrotto SuperClamp can be adapted with a 3/8 stud to support a Nikon D800/16mm f2.8/NN RS-2 ring mount, shown in View A in a helicopter cabin. For the nadir shot, a Manfrotto SuperClamp/Magic Arm/Camera Plate is independently attached between the mounting tube and the camera, shown in View B. Finally the quick release on the 16mm lens ring is loosened so the NN RS-2 and its clamp can be removed, leaving the camera suspended and looking down with an unobstructed nadir view, show in View C.
In this situation, taken at the same no parallax point (NPP), the nadir shots are treated like any other and will stitch on the first pass without viewpoint correction. The finished panorama looks like this:
Careful handling of the camera, firm mounting and a skillful transition are important if objects are very close. Note the stitch error on the tube just below the NPP. The clamp rotated a small amount during the switch between mounts. With the tube only about 30cm from the NPP, the image is particularly sensitive to parallax. The cabin floor shows no error, as it is farther away. Another cockpit panorama made in this way except that a tripod fit the floor for all images except the nadir:
Finally, these Manfrotto products show up frequently at good prices on eBay, as many probably cannot find an application for them.