Craig did shoot the idea or Bonds 24 and 25 being a two-part story, but that does not mean there cannot be plot threads that tie them together - those being Ol' Ernie & co. He appeared in 4 of the Connery Bonds and those films were 99% stand-alone stories but with a mutual source of threat. And to make Blofeld work in the 21st Century Logan has to go back to the source, that being the Master Ian Fleming. No nehru suits or white persians, just a large middle aged man who'se mind is like a black diamond.
Yeah, the media and fans took that original piece of news too far. It mentioned that Logan pitched an idea for Bond 24 and 25 having a connecting "story arc" if I recall correctly. They are many different ways that two films can have a connecting story arc WITHOUT being a two-parter filmed back to back. As you mentioned, the early Connery films and their focus on Bond fighting Spectre can easily be classified as having a connecting story arc and yet they are still very much stand alone films as well.