In Indesign there is no way you can directly work on the XML-IN footnote, since indesign won't support XML tags in footnote stream.
To achive that you need to have XSLT/Perl/Indesign Scripting.
This task is achievable, you can create a auto footnote for XML workflow projects.
1. Create an XSLT to transform the footnote to the respective places
2. Change all the "<" ">" to some standard names, since indesign won't accept XML tags in the footnote stream.
3. Import it in indesign and using script convert it to autofootnote.
Shaji
