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These swaps are clearly "non-organic" (i.e. didn't emerge from gradual changes in colloquial language). Are they the result of a change in editing staff? Spelling correction software?

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They updated their style guide.

Are the style guides updated to reflect the public use of these words? If so, I imagine if we were to graph the change in use over time in the public would be a much more gradual and organic one?

Yep, as the Google N-Gram view in the article shows, usage of "theater" overtook "theater" in the late 1970s, but the two had quite similar usage rates from the 1940s onwards.

Style guides generally update to represent the editorial team's preferences, to reflect changes in the wider world (e.g. see the comment in this thread about "Constaninople"→"Istanbul", or to make a point (see the New Yorker's continued use of diaresis in coöperation etc.[1])

[1]: https://en.wikipedia.org/wiki/Diaeresis_%28diacritic%29#Engl...

In 1961 there was no spelling correction software.

"In 1961, Les Earnest, who headed the research on this budding technology, saw it necessary to include the first spell checker that accessed a list of 10,000 acceptable words."

http://en.wikipedia.org/wiki/Spell_checker

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