The answer to your question is this. It is possible to stitch an equirectangular panorama or a stereographic projection from handheld offset images but you are likely to end up with problems like the one in your images, especially when you are that close to things you are photographing.

You see the problem with the ceiling may not necessarily be connected with the image offset. The software may not be able to find control points on plain surfaces without any features and therefore will not include this part of the image in the output panorama/projection. I use a variety of stitching software and whenever I'm shooting indoors, I often have problems with stitching the ceiling.

That's why if you are serious about your projections, especially inside buildings, buy a dedicated panorama head and use a sturdy tripod. Then, you images may have fewer control points due to the lack of features but the software will still stitch them and will not have any problems aligning them either as the parallax error is minimal.

I'm not saying it is impossible to shoot and stitch a good panorama/projection handheld (I did that a few times) but in my opinion it is not worth it. You will always waste time on photoshop correction and control point optimisation due to parallax errors.

Also, consider switching to a more dedicated stitching software such as AutoPano Giga. Just a friendly suggestion.

Check out my photostream for my stereographisc and equirectangulars and if you have any more questions just ask:

http://www.flickr.com/photos/grzegorz_rogala/sets/72157619963655050/

http://www.flickr.com/photos/grzegorz_rogala/sets/72157626316921040/

Best Greg