Footnotes are basically float-after areas. Both float before and footnotes are not much of a problem except for multi column layout (and, well, in tables). In multi-column layouts, the equal width of the column should allow reassigning content after decreasing column height without doing a complete re-layout. Side floats, of course, are a real pain, especially if you want to do conflict resolution properly.
I'm still attached to my proposed footnote processing method as described in the alt.design notes.
http://xml.apache.org/fop/design/alt.design/footnotes.html
I'm looking at extending it to cope with footnotes in tables within columns.
Peter -- Peter B. West <http://www.powerup.com.au/~pbwest/resume.html>