On the simplest level, like Mike Figgis's Timecode which similarly juxtaposed action in separate screens, longueurs in one episode such as lengthy driving sequences or pauses in conversation coincide with important action in the other and the shots and themes really do talk to one another.
But there's much to it than that. Alex Fulton has a length explanation for this theory with plenty of evidence along with how it effects the narrative to create a happy or at least satisfying ending:
"Herein I will suggest my own opinion, based on a unique reading of the material, that the ending is in fact of the happy variety: Cooper wins. Having said that, the way the events are depicted works like a puzzle with its pieces all out of place. Using a little bit of that intuition Agent Cooper so often employs allows the viewer to lock the pieces in place. A rearranging of the events of final two episodes gives the viewer a more satisfyingly optimistic conclusion, albeit one that does not resolve in the traditional way of most television. It requires some work on the part of the audience—not a strange concept in avant-garde art—to properly formulate."Here's are some of the key moments:
And a focus on the ending in particular:
It's remarkable how the final shot of the forest in #18 is the exact length of the closing credits in #19 and the experience ends with Julee Cruise on #17 which just happens to be two minutes longer.