Ed:
I use both autopano Pro (Kolor) and PTgui, along with CC for stitching with P1 files.
Autopano will have problems with the exif info, as for some reason, C1 does not export it the way it's needed by Autopano Pro, PTGUI seems OK. But even PTgui seems to have problems seeing all the focal data, from a tech camera, since the lens info is missing and PTgui will ask for the sensor size sometimes and other times it sees it correctly. But both tools allow for an easy way to input the data when needed. I seems that both companies are not looking much at the Phase One files when writing the programs.
I have found that most inline stitching CC will do fine, but there are certain times where I have a lot of color shifting even with the LCC correction in C1, (mainly with the 40mm Rod and blue skies), where I can't get a good blend with CC, especially if I had a CLPL on. With nodal pans from a tech camera, the wider the lens, the less likely CC will get a good solution even with a pretty good nodal placement.
PTGUI and Autopano work better on nodal pans, as they give you a lot more solutions to pick from. They also work much better on multi-layer stitches, like 6 ot 9 shots, where CC seems to both get bogged down and lost at times. CC's engine is pretty much the same as CS5, I see no changes or differences in results between all of them. Where as both PTGui and Autopano make a lot of upgrades.
Exposure blending again I often will have to work with all three at times to find one tool that gets the best solution. Solid blue skies with a lot of gradient to the sky will be the most problematic, and PTGui works very well here.
All 3 work fine on 16 bit images (but CC can bog down on multilayer stitches in 16 bit for me) I am windows based all 64 bit.
You will find a ton of control features in both Autopano and PTgui, none in CC, Both tools I feel would benefit from a better user guide, but I have basically learned by trial and error. Autopano has a nice video guide that can help.
I just finished what I though would be a simple 3 part from a 15mm L C and 15mm R stitch, that I ended up having to use both tools to finally get a good solution. But most times I get a clean one the first time.
I would consider both of them, along with CC.
Paul