The only real change the hekate_ipl.ini file needs is the nosigchk line for each of the MMCs, be it sysmmc (CFW) or emummc or whatever the user uses.
I include because most of the stuff in the IPL file, while not being configured, already has that line set and ready for the signature patches.
All that would be needed is for the user to redo their Hekate configurations when Hekate boots up, that's it.
Once you do that setup once, you no longer need to copy over the hekate_ipl.ini file from the package.
I only copy the patches folders inside atmosphere and the patches.ini for bootloader on each update for my system, that's it.