I concur, back then, in the 1960's it was definitely make it up as you go along era.The writers guide was intended for prospective writers to get a handle on the baseline of the series concept before writing their assigned story. It wasn’t a technical treatise and encyclopedia with hundreds of pages of minutiae for fans.
You’re ascribing modern television storytelling sensibilities to a show from the 60’s. Gene and co were making this shit up as they went. There was no overarching plan.
I'm glad we're long past that era.