BART cops are real cops. They are not security guards. The reason for the seperate agency is purely to avoid problems of jurisidcition.
http://www.bart.gov/about/police/
The BART Police Department is comprised of 296 personnel, of which 206 are sworn peace officers anywhere in California. Its chief of police commands the department that is BART's sole law-enforcement entity and provides the full range of police services. To prepare for major emergencies, critical incidents, and tactical responses, the department is a signatory to the Bay Area's mutual-aid pacts and has teams of highly trained officers for tactical response and/or crisis negotiations.
Community-service officers, communications/9-1-1 dispatchers, revenue protection-guards, and clerical staff and supervisors comprise the department's civilian employees. Qualifications and training for BART police officers exceed the guidelines of the state's Commission on Peace Officer Standards and Training, which certifies all California peace officers. In addition to meeting POST requirements, every BART police officer applicant must have completed at least a year of college. Most officers are assigned to the Patrol Bureau and become eligible for specialized assignments, including: field training officer; canine handler; SWAT operator; detective; bicycle patrol; personnel and training officer; applicant background investigator; crime analyst; administrative traffic officer; FBI Joint Terrorism Task Force investigator; and undercover anti-vandalism and special-enforcement teams.