this is because it is more complex than it looks like
Ubuntu core has a bunch of dependencies on the bootloader and the partition table to support the following Ubuntu core features:
* rolling back to previous image when upgrade failed
* full system upgrade
as such the 'boot' device , e.g. /dev/mmcblk0 (EMMC) vs /dev/mmcblk1 (SD CARD) must be hardcoded in a few places.
It is very likely possible to install Ubuntu core on eMMC, but you will need to find out where to make these changes. Ubuntu core also uses its own partition table , so you will need to create the partition table on eMMC..
if you want to experiment with that, i would recommend asking the ubuntu people on #ubuntu-arm .