And for that matter, why would the Great Beings (or whoever created the Toa) have to have programmed the Kaita into the Toa in the first place in order for the Kaita to exist?
The GBs were never portrayed as omniscient, omnipotent deities. The Kaita forms could be something the Toa achieve in a spiritual manner as opposed to being programmed into them. Again, the Toa are part organic. They have some sort of soul to speak of, and that aspect needs to play a part.
Nobody's really talked yet about why the Toa exist in G3 in the first place. If they were initially created solely to deal with smaller threats (in which case larger, more powerful entities would exist elsewhere), then that would explain why the GBs didn't just make them Kaita. But the whole point of the Toa is that they grow and learn over time, overcoming the boundaries that were intended to keep them in place and breaking new ground in the process.