Budgetary reasons. Why would the FBI spend their own money and resources to enforce FDA regulations? That's money coming out of their budget. There would need to be in place a central federal police force that would be funded by the various agencies that require X number of hours of law enforcement per year. But this might create even greater costs due to the overhead in running this federal police force. You would need offices all over the country alongside the current federal agency offices like FDA, FBI, DEA, etc.

It would probably be easier to have the FBI setup as a federal police force which it pretty much almost is. Agencies could send part of their budget to the FBI to essentially purchase law enforcement hours. Factor in the cost of hourly rate of officer + hourly rate of overhead for officer + usage of resources + any other expenses incurred and then bill that to the agency that requires the police work. This would help smaller agencies by reducing the costs they would have to spend on maintaining a police force of their own 24/7. The only issue would be that the FBI would need to maintain a force large enough to enforce anything the other agencies would require of it. Things like DEA work and regular FBI work would require much more man power than things like DOE work so smaller agencies might not get the representation and priority they would get by maintaining their own force.