(as stated in bug 714733 comment 105, Footer.html should be actually in content).
Because if a theme wants to style the chat panel, it also has to include the Footer stuff, including the .js files, as they are all located in chrome://messages/skin/.
Footer.html and the js inside of Footer.html is not allowed in chrome://messages/skins/ (because of security reasons).
So the concerns are theoretical and not because you've actually seen something not working?
The files of a messagetheme aren't shown directly. They're html snippets for a message/content message/the conversations 'footer'/... They are loaded from their (chrome-)URIs as text, parsed and inserted into a browser to show your conversation.
(In reply to Alfred Kayser from comment #4)
> I have created several themes for Thunderbird, such a LittleFox, Nautipolis
> and Walnut. These also have styling for the chat panels. As this also needs
> This is refused by AMO,
Was your updated theme rejected by an automated process, or by an AMO editor?
> and when imported into a Thunderbird this
> longer works.
That seems very surprising, as the current Footer.html is in skin already (http://mxr.mozilla.org/comm-central/source/mail/components/im/jar.mn#31).
If you still think this file is causing an issue, I would need to look at your theme to understand what's going on (so either attach here, or email to me the version that contains these changes and that is refused on AMO).