My vote goes for "the creators of the show never cared and thus never knew", the one thing for which there is rock-solid evidence.
Oh, wait, that has been left out of the choices for some reason...
Okay, it's the "combination" thing, then. Clearly, the flow of antimatter flow takes place in the secondary hull ("That Which Survives"), in addition to potentially happening elsewhere. If the antimatter pods are in the nacelles, what business would the fuel have in the secondary hull unless it went there for rest, recreation and reaction?
Basically, the one problem we face with the TOS ship is finding a part of it that does not
have antimatter within! Even the saucer seems to have some, as per "Errand of Mercy".