Are you actually asking if gameplay decisions lead to maps developing differently?
You talk about the natives reacting differently depending on your exploration.. yes I think this is fine and as It should be.. they are a dynamic system responding to your actions.. but I feel the "starting villages ...

Following a mysterious crash, that may or may not have involved The Captain sharing a bottle of whisky with the chief engineer, 2 brave survivors create machine and science, trying to resurrect technology from the very rocks around them.

To save sanity Captain Twitchi and science officer Z Tech ...