Sorry if bumping such an old thread is rude, I just want to leave this here to help anyone else who had my problem.
I found this post while trying to apply kernel options on my UEFI install, and it did not work when copying the instructions here verbatim because UEFI installs use a different grub.cfg.
I posted my solution for UEFI custom kernel options here.
Basically you do the same process that was outlined here, but you output the config file to /boot/efi/EFI/qubes/grub.cfg instead.