You can do it, but not using our installer.
LE requires two partitions: one for /flash (boot files) and one for /storage (persistent data) and on x86_64 hardware you can use MSDOS or GPT partition schemes. The boot volume can be either vfat or ext4 but storage MUST be a linux filesystem type (ext4) else we cannot set secure SSH key permissions and you'll never be able to login to the device console.
If the current filesystem is a Linux format then you can use Gparted from e.g. an Ubuntu Live USB image to shrink/move the current partition to make space for the /boot volume (512MB is enough) and mount the existing partition as /storage. Install syslinux or GRUB to the boot partition with an extlinux.conf that sets boot=/dev/sda1 disk=/dev/sda2 etc. and then copy the KERNEL and SYSTEM files over, and on first boot we will (re)create the .kodi and .cache and .config folders that we need on /storage.
If the current filesystem is a Windows format then you need to create TWO partitions so that we can store Kodi data correctly etc. - the media partition will auto-mount and be usable. I'd create the /storage partition at 8GB .. it's normally enough for all the thumbs and other cruft that Kodi accumulates in use.