On the roof: higher CoG, more wind resistance, less convenient to fill, easier to drain fuel to the main tank (if located at the right place on the roof), if there's spillage, less easy to clean up, although perhaps easier to see a slight drip.
At bumper level: will increase polar moment of inertia, with negative impact on handling and dynamic departure angle, easier to fill, less convenient for fuel transfer to main tank. If there's spillage, you may not see it at first and will potentially be adding to skid risk on surfaced roads. If "rear-ended" the storage cans are far more likely to be damaged...!