It's a chain of command (i.e. BART police report to BART, Campus police report to the school, way less messy than BART or the school having to convince the jurisdiction how to police the area) and prioritization thing. Bespoke police agencies exist to police their niche to an extent that would be unjustifiable if it were coming your normal police department and taking resources away from their other tasks.
Transit police, campus police, DEA, ATF, etc, etc, etc. Their entire job is to harass people that the equivalent generalist police couldn't justify allocating resources toward.
Irate homeless? SFPD won't show, but BART Police will.
Drunk college kids shenanigans? Normal cops don't care, but campus police does.
Weirdos making machine guns or huge amounts of LSD? FBI don't care as long as you're not trafficking, they got real crime with real victims to chase. ATF and DEA care though.
Wash rinse repeat this pattern for literally every bespoke police agency.
Yeah, jurisdiction can be a theoretical reason for these agencies but once again it's still a priority thing. When agencies care jurisdiction and coordination isn't a problem. Having one agency span multiple only helps if you're chasing stuff so petty it would get dropped.