For this antimatter transport experiment, they only transported 92 antiprotons. To store and transport that, the requirements for the magnetic field and vacuum are many orders of magnitude lower than what would be needed for macro-scale quantities.

Also, if there was an accident and all those protons annihilated, the consequences would be unnoticeable except to sensitive instruments. The energy involved is about one seven billionth of the energy in a single grain of gunpowder.