I'm fairly certain that Nintendo has settled with a split-time-line for the chronological order of their games. However, I also suspect the the greatly coveted 'top-secret grand time-line' in their possession is a slightly cleaned up version of something they haphazardly jotted out on a bar napkin, complete with Saki stains.
Given Nintendo's history of thinking 'game-play' first, 'story' second; I find it hard to believe that they've spent even a fraction of the time the fan-base has in examining all the in-game minutia to find a suitable order for the games. My suspicion is that if we were able to take a look at their actual time-line, we'd either find that it had some pretty hefty and unsatisfying holes in it, or that it was a slightly tweaked version of the most widely accepted fan made time-line. I also don't see them releasing their time-line to the public in the foreseeable future, as it could possibly create issues for slotting in new games later on. In addition, I believe that Nintendo is well aware of the constant and self sustaining fan-speculation, and that they wisely recognize it as a good thing.
For my part, I hope they never release their time-line, split or otherwise. I don't think I'd be entirely satisfied with their version of the chronology, and most importantly, I'd miss trying to make all the pieces fit.