Currently, auto-commit can be enabled at the time of subscription via CLI, UI or REST API for single tenant framework cartridges and at the time of cartridge deployment for multi-tenant framework cartridges.
However, auto-checkout can only be enabled by updating the init.pp file in the puppet/modules/agent/manifest/ directory. Thereby, auto-checkout once enabled will be applied to all cartridges. Currently, users will not be able to enable auto-checkout for some cartridges and set the web hook other cartridges.
I have created a JIRA  regarding this proposed improvement.