Or Spock could be just listing separate items since he doesn't directly connect them by saying: "Blast damage in decks ten and eleven resulting in minor buckling in the antimatter pods and light casualties."
True enough. But the general gist of the litany is that damage was minor, not extensive. We saw hits slamming to the immediate vicinity of the torpedo launcher; if there were further hits (into the warp nacelles, say), the "light casualties" thing would be a bit less likely.
The evidence can be used in many ways, but one way is to tie together "antimatter pods on Deck 11", antimatter-warhead torpedoes, and the idea that not all antimatter pods (decidedly plural!) aboard the ship need be located in the same place - and certainly not limited to the two pod-like things dangling at the ends of the external pylons!
TOS dialogue seems to verify that main power and the flow of antimatter fuel is dependent on key instrumentation in the engineering hull, but there is also evidence that the warp engine nacelles may contain antimatter either at times, or then all the time. What would the antimatter be doing up there if not annihilating and generating power?
It's possible that the TOS ship features an "afterburner" of sorts - that annihilation happens in the "That Which Survives" location, but that one gets extra oomph by channeling some antimatter directly into the warp coil system. There seems to be a distinct lack of situations where the warp nacelles would threaten to explode and would have to be jettisoned for that reason; this rather speaks against the continuous presence of antimatter in the nacelles.