From an official Nintendo Magazine interview with Eiji Aonuma:
“'Yes there is a master timeline but its confidential document!' explains Aunuma-san. 'The only people to have access to that document are myself, Mr. Miyamoto and the director of the title. We cant share it with anyone else! I have already talked to Mr. Miyamoto about this so I am comfortable in releasing this information – this title [Skyward Sword] takes place before Ocarina of Time. if I said that a certain title was ‘the first Zelda game’, then that means that we cant ever make a title that takes place before that! So for us to add titles to the series, we have to have a way of putting the titles before or after each other.'”
Here's the link:
Skyward Sword Before Ocarina of Time in Zelda Timeline
Since Aonuma apparently asserted several times that an official (and thus canon) timeline existed, I feel inclined to rule out the possibility that he would allow the release a timeline which was somehow not official. The only way I can see that being even remotely possible is if Aonuma had no creative control over Hyrule Historia.
But according to a Kotaku article:
"The added translations also reveal that the book's 'supervising editor' was none other than Zelda boss Eiji Aonuma, so yes, this is as official as official gets.'"
Here's the link:
The Official Zelda Timeline, Now With Added Detail
What more can be said? At present, there is simply too much evidence in support of the idea that the timeline is official (and thus should not allow for contradictory theories). I think the only "room for interpretation" is the glaringly obvious amount of empty space between each game; it's up to us to decide just how much the games relate to each other.
Additionally, Nintendo can obviously place new games anywhere they want on the timeline from here on out. I think that's the only creative freedom they're defending right now; they reserve the right to place new games anywhere in the chronology, but the "official" order of currently-existing games should (I imagine) remain unchanged and undisputed.