I guess a fueling station or a tanker could beam antimatter into a starship in a constant stream without bothering with packaging it inside a series of containment vessels, as anything being beamed appears to be in a form that cannot interact with its surroundings much. It effortlessly goes through walls, after all!
The big problem would be getting the beam through the walls of the antimatter tanks at the respective ends, though: if the tanks are protected by forcefields, then the transporter cannot penetrate.
If, however, the tanks are protected simply by electromagnetic fields, then the transporter probably can penetrate, at least after some tuning. But it takes more handwaving to explain how EM fields can contain electrically neutral antideuterium than it takes to claim that forcefields (based on unknown principles, but demonstrably capable of containing electrically neutral matter) can.
As for the "Peak Performance" bit, I don't think there's fault to be found in transporting antimatter in a package that is in danger of rolling to the floor. After all, regular means of packaging antimatter appear to be quite secure against accelerations of thousands of gees, disruptor fire, and the occasional divine intervention... No doubt Wesley's story about the vulnerability of the container was pure bullshit.
Of course, we don't really know whether Wesley beamed aboard a quantity of antimatter, or possibly an alternate energy source for the warp drive. For all we know, his experiment contained a quantum singularity.