I assume any future antimatter based propulsion would rely on some sort of metastable particle pair that are made up of matter-antimatter components like protons, except one that can be more easily/efficiently split and recombined. Otherwise the factories will just blow up the first time there's a serious accident or containment failure.
Just as an example: imagine particle A made up of up, bottom, and strange quark and particle B made up of down, charm, and top quarks (I'm ignoring charge) that can be stored without interacting. The engine splits them into quarks that then can annihilate each other (AFAIK that's not how quark plasmas work but you get my drift).
