Since fmon is usually started by on-animator.sh, and on-animator.sh started from rcS only after the update block is passed, one would have to start fmon another way.
It is easier, I think, to edit rcS to the effect, that it deletes the update files if it finds a KoboRoot.tgz, and runs the update script block, if it finds a xKoboRoot.tgz (in order to allow to install updates and applications using the update mechanism if one wishes).
Somehow related: I did a new version of my
kobomenu and also of the sample application "start menu". It gives you the choice to select on start up, whether to install an update or to delete the update files. I will upload the new version after some more testing after the holidays.