There are also references in TOS episodes the provides as much if not more instances where the nacelles contain the main power generation, or at the very least significant power generation. So that intent of having the nacelles containing power generation is indeed how it ended up on-screen.
If I'm allowed (?) I'd like to add
The Ultimate Computer
SPOCK: M-5 appears drawing power
directly from the warp engines, tapping the matter-antimatter reserves.
SCOTT: So now it has virtually unlimited power. Captain, what'll we do?
By Any Other Name
SCOTT: I have opened the control valves to the matter-anti-matter nacelles. On your signal, I will flood them with positive energy.