Firstly, PTGui is a freak, it's an amazing software app.. It just works and works well.. However, APG for your case could work much better since ACCORDING TO APG, your NNP is not correct.. Its heaps out.. APG detects very differently so its not as tolerant if your NNP is out.. Saying that, it might not be out..
It must also be pointed out that APG has many more features than PGTui and if working as it was designed it would be the best and most advanced stitching software. I went off using APG for many reasons but I was forced back to it when I wanted to try out the LivePano..I have spent weeks and many many hours in trying to get APG to work for me so I can finally test LivePano.. I have decided to move on from using the Fisheye lens and will therefore be doing some test panos using my 50mm.. That opens the gate to other issues, namely RAM... I would have tried it in the beginning but my poor old iMac locks up or APG will crash if it runs out of RAM..
I have battled over this for over two years in using my 10.5mm Fisheye Lens.. Your Zenith and Nadirs seems to be perfect according to these cube images below from PTGui. However, according to these cube images below from APG, your NNP is out.. But is it.. The cube faces for the Nadir and Zenith would suggest it is way out.. But.. I do not think it is as far out as APG might suggest.. It might well be APG creating the illusion that the NNP is out, since it gets confused with Fisheye Lenses.. So you could spend hours.. days... week.. or in my case, YEARS in trying to work out what I might be going wrong.. So much time wasted.. Its not out. My NNP is perfect... I have tested it with other stitching software too..
I achieve the same kind of RMS as you do, but the RMS is a really bad indicator of results.. I achieve the same kind of results as you do with BOTH APG and PTGui... I use a Robotic Head, and one of the main reasons why I went in this direction, was very much driven by the fact that I could NOT achieve a good result with my NN4 and 10.5 Fisheye Lens when using APG to stitch.. I then purchased my VR Drive only to find that I had the same issues as before.. I then began to use PTGui.. Perfect.. Not a single issue.. The new APG apparently has fixed the many issues.
One reason for your rendered images being different sizes is due to the fact that PTGui renders at 300dpi and APG renders at 240dpi, which does not make sense to me.. In my opinion it should render at 96dpi.. You cannot view 240dpi on most monitors.. 300dpi would be the minimum for print.. Anyway.. besides all that... There is still an inconsistency since if I put the PTGui rendered pano to 240dpi, its still not the same size, so something is wearied...
This url below shows that your NNP is out.. But as I said, 'IS IT'... Or is it APG creating the illusion that its out since it cannot cope with a Fisheye Lens in the same way as PTGui can... I really feel that the issue is really the Fisheye Lens.. APG does not really know how to interpret a Fisheye Lens.. If I use my 50mm or even my 35mm, the nadir looks much better and the stitching is also much better.. Therefore, it would suggest that it's the Fisheye Lens which is the main issues. Others on this forum do not get the many issues you get or I get.. BUT, some of them are using a 85mm or other prime lenses.. http://www.destinyvirtualtours.com/Harry/HarryNNP.html