^That's right. As I said, it's incompatible with what the characters in the episode believed to be true, but beliefs can be wrong -- especially beliefs about history. Just because a character in a story says something is true, that doesn't absolutely prove it's true. Fictional characters can be mistaken in their beliefs and conclusions, they can be misinformed, they can be liars, or they can be deluded.
Just three points:
1. There seems to no disbelief by Reger and the other gentlemen with him when Kirk says they come from the valley. So this would be indicative of more than one settlement on Beta III.
2. Never once does Spock make a connection between the technology and Starfleet technology like in the comic.
The Return of Archons wrote:
SPOCK: And apparently commanding powers far beyond our comprehension.