OK, I just tried to create a Word document sized 9x12cm and copy/pasted
http://strobist.blogspot.com/2006/03/lighting-101.html into it. Everything worked fine until I tried to print it out with CutePDF. The output PDF is sized A4 with the content centerized with 9x12cm in dimension. I set the paper size in CutePDF to 9x12cm as well, but nothing better came out of it.
I'm not trying to battle here which is better, but I just found that with my app even though I had to copy/paste content to it, it did create clean chapters along with bookmarks. btw, how do you create bookmarks with CutePDF?