Changing the database configuration currently requires access to the machine where the cluster node is running. In many cases, it creates too much burden because there are more people who have access to the database compared with the number of people with physical access to the box. Particularly, it is 100% relevant for ES Cloud as those machines are completely locked for customers.
Certainly, not all the settings can and should be changed via the API, and some settings also require for the node to restart, so it needs some research.