The rationale of separating the baseband processor from the main processor (known as the AP or application processor) is threefold:
Radio performance
Radio control functions (signal modulation, encoding, radio frequency shifting, etc.) are highly timing-dependent, and require a real-time operating system.
Radio reliability
Separating the BP into a different component ensures proper radio operation while allowing application and OS changes.
Legal
Some authorities (e.g. the U.S. Federal Communications Commission (FCC)) require that the entire software stack running on a device which communicates with the mobile telephony network must be certified. Separating the BP into a different component allows reusing a stack without having to recertify the full AP.
Since the software which runs on baseband processors is usually proprietary, it is impossible to perform an independent code audit. By reverse engineering some of the baseband chips, researchers have found security vulnerabilities that could be used to access and modify data on the phone remotely.[3][4] In March 2014, makers of the free Android derivative Replicant announced they had found a backdoor in the baseband software of Samsung Galaxy phones that allows remote access to the user data stored on the phone.[5]