I personally would probably go with a build-in-build, and put some
form of application rootfs on the emmc - this could either be a simple
chroot or some more advanced form of container. This avoids nasty
breakages and update problems when the filesystems go out of version
sync. Other techniques might also apply depending on your software
rollout process, like an addtional overlay fs, or a pivot-root with
initrd, or.... it depends. But ripping out random packages and
rearranging them at random locations certainly isn't a good idea. It
already hurts when I think of the mount-and-deploy magic one would
need for this to roll out in production.

My $.02