A certificate bundle essentially provides a list of trust roots. It tells the agent who to trust when communicating with the backend.
Many customers run in docker. Sometimes, those images don't provide their own certificate bundles because the images aren't usually used to communicate over HTTP. We provide our own bundle so that customers have an easier time installing the agent.
When system certificates are available, the agent will default to using those over the included certificate bundle. The certificate bundle is only used when no certificates are provided by the system.