Secret History ideas a response or precursor to The Return?
I assume most people who don't regard the Secret History as canon either don't regard Mark Frost's contributions as important as David Lynch's or believe Frost came up with many ideas for the Secret History after the script was written or primary shooting completed.
It is also possible that Frost had many of the Secret History ideas before The Return was written. These ideas would have certainly informed his approach to the script.
As is frequently pointed out, David Lynch said this in regard to Frost's book: "I haven’t read it. It’s his history of Twin Peaks." It would be interesting to know if Lynch knew what Frost's ideas were of this history while they were working on the script. Lynch is always very direct about Frost's role with the show and I imagine some important aspects of the history were discussed. http://ew.com/tv/2017/01/09/twin-peaks-david-lynch-press-conference/
There are so many fan theories being discussed that it seems important to consider the history developed by the show's co-creator when considering any theories.