Chris,
Were the singles taken vertically or horizontally?
Having used Ptgui and Autopano for years now, I personally don't agree that they can make a better image. Where both Autopano and Ptgui break down IMO is in the exposure blending. Often times both tools can't get a sky even especially a sky where the light is fading across the frame.
There is more user interaction available with both Ptgui and Autopano, but I have never really been able to do much with it. Autopano has some good video's but even then when you start really getting into the techno parts of the shot it can be very difficult at least to me, more time than it's worth, and then after all is said and done you don't get a good blend. And with Ptgui, that's using the enblend plugin. On the flip side, with CC panoramas, at least with Fuji X-trans tifs, the final output to me was always softened unlike Ptgui and Autopano. I had switched over to those tools for Fuji files due to the softness problems with CC. Now that it can all be done as a dng inside of LR, that issue is gone.
To me it's a balance of time needed and what's the net output going to be worth, as more and more folks are willing to accept a pano from the iPhone as top end.
What LR has to me is a better overall solution, sure it could use some fine tuning, and maybe that will come later. But the ability to have the image as a dng and then work it with the LR toolset is worth a lot.
The rail bending in the foreground is possibly also due to the lens, I would need to see the original images. But there has to be some curve there or maybe it's a 90 degree bend? The railroad track also pick it up to a degree. Some of this can be fixed by warping the final image in CC or using the Len correction tool on the final shot.
I don't think that a nodal solution would have fixed the curving of the rail. The only solution I can think of would be a shift lens setup.
LR and CC both to offer a better exposure blending in most cases than either Autopano or Ptgui, where the later are going to give you more options to fine tune the distortions.
I have been a stitcher since 2002 or so always to gain more overall resolution, not as much for the pano look. But the tools that are available now are excellent.
Paul