You can do furigana with no 3rd party apps. Actually is very simple.
In pages or word, simply have an extra line with smaller font for the furigana. There is no mystery about it. Please look at the pdf I post in the 1st post.
Otherwise, you can add the furigana simply by adding a text box and freely moving it in the text, just like if it was photoshop, except that here you can export as a pdf and have the zooming features of a pdf.
This is with the 1st method I mention, http://www.mediafire.com/?fe70dsbxtyt
This is with the 2nd, more flexible method, http://www.mediafire.com/?dygjc99fxys
Sincerely I do not see why you said it cannot be done.