The unpacked config file and the cpio is what you want there.
The cpio is an archive format, just like tar is. It contains the part of the ubiboot FS that has the menus and the launching system.

If you want to use the kernel-plus you also need to unpack the related modules to /lib/modules/2.6.32.54-dfl61-20121301
If you want to use the kernel-plus_NAT you also need to unpack the related modules to /lib/modules/2.6.32.59-plus_nat-20121301 directory.

Also, do not forget to edit the kernel locations and names in ubiboot.conf.

For example, if you have a kernel named "/boot/zImage_foobar" and you want to have a menu entry "My foobar kernel" as the first line in the ubiboot menu, you could put something like this in ubiboot.conf:
G_HARMATTAN_1_LABEL="My foobar kernel"
G_HARMATTAN_1_FILE="/boot/Harmattan/boot/zImage_foobar"

If you want it as the second entry, put the lines in G_HARMATTAN_2_LABEL and G_HARMATTAN_2_FILE and so on...

You need to have the so called "l2fix" in the kernel to make it boot up faster.
There are lots of kernels that have this, for example the latest Nitdroid kernel from e-yes, and the harmattan-plus kernel from Hurrian have this.

Well it could easily be implemented. I made a test cpio for Farfry which has a menu entry for backup tools, but it needs some work before being useful. As I recall there were 2 requests by Farfry for features not implemented in ubiboot yet to make it possible to do it, bmestat and sshd. those are still under construction.