This was originally discussed on the mailing list with the subject the same as the summary here, but the discussion got a bit derailed.

Copy/paste from Daniel Drake <drake@endlessm.com>:

Hi,

I'm looking at migrating to a setup where /boot is on the main root fs
partition (ext4), rather than being a separate partition. This is for
simpler partitioning, and for space savings (otherwise the same
kernel/initramfs is stored separately on 2 partitions).

Adjusting my build tools with this in mind, the resultant ostree boots
fine. However, once booted into the deployment, /boot shows exactly
what was committed into the deployment. It does not show the
ostree-managed bootloader setup, which is visible at /sysroot/boot.

This breaks standard usage of the 'ostree' binary as it expects to
find bootloader configs in /boot/loader.X etc.

I wonder if it would be acceptable to modify ostree-prepare-root to
account for this. When preparing the root, if we find /boot/loader on
the real disk, automatically set up an appropriate bind mount inside
the deployment, so that /boot reflects at what I'm now seeing at
/sysroot/boot.

Other options include having the /boot inside the deployment as a
symlink to /sysroot/boot, or having the software inside the ostree
create an appropriate bind mount during early boot, but those options
are less attractive to me as I must also support upgrades from earlier
installs, where /boot is separate, so things get a bit more tricky.

Daniel