Maybe you can have the script change the about:config file (or run a macro to do it) for firefox as well.
You will find bookmarks.html in %APPDATA%\Mozilla\Firefox\Profiles*.default folder on many windows boxes. http://kb.mozillazine.org/Profile_folder_-_Firefox
First get a hard location for that (without the wildcard *) or move it, and make the changes. Unsure about over network, but just test it out.
From that same folder you have prefs.js which is the same settings from about:config in firefox.
Add line to prefs.js:
Manually in firefox:
open about:config in firefox
right click in the window (any of the fields, but in the middle somewhere)
add "browser.bookmarks.file" and the location "<BOOKMARK_LOC>"
haven't tested either way yet, but that would be the way to go.
EDIT: I misread question. Thought you wanted shared bookmarks... You can just edit the bookmark.html in firefox profile folder.
EDIT2: ANd that was windows and not unix/linux. Either way, on linux it's easier. I was coming back to say where in the installer to change.
This is untested also, but I can probably test this later, because I have a Linux box I can change. You can open the installer and change the following:
Before you run, create <BOOKMARK_LOC> with the bookmark.html (I think you need bookmarks.bak too)
edit "<zipped installer>/firefox/defaults/prefs/channel-prefs.js"
add "pref("browser.bookmarks.file", "<BOOKMARK_LOC>");" to the end
Again, haven't tested, but will probably be able too later.