This post still confuses me. /boot not being mounted has nothing to do with grub. Grub uses its own abstraction layer to read grub.cfg which points it to a initrd/kernel. This "abstraction layer" never "mounts" anything, grub has no knowledge of mounts. So only your grub.cfg could be wrong, or not written because you didn't manually mount /boot, but pretty sure boot-update automounts /boot so grub-mkconfig can write grub.cfg unless specified to not automount.