You should read the threads... part of it was just artistic. Kind of like watching a Twilight Zone episode or reading Slaughterhouse Five (Vonnegut).
The time-out-of-sequence imitates the disorientation Kyon feels in this situation.
The other reasons are more mundane.... organizing the events that way leads up to a climax that lesser beings can handle (oooh, monsters! and Kissing! ... the world is returned!).
I found the Kyon order very satisfying for a first view... but when I rewatch it I usually follow the chronological order because I find the "daily life" and that last "rain" episode very pleasant to end out on.
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