Hmm, I've never seen that FS translated article. I don't know why I put FSA in the CT when I've always put it before OoT.
Though there was an interview where Aonuma said (during FSA's development), and I paraphrase, "FS was intended to be based before OoT, so FSA probably will be too." This was before Miyamoto came in and changed the story of the game by removing the Master Sword, etc., so at least from this interview it can be inferred that Link was not necessarily the same as FS Link.
Also, I still see no concrete connection implying that ALttP and LoZ/AoL are in the same timeline outside of Miyamoto's timeline from 1998.
ALttP—CT:
- Landlocked Hyrule
- Seven Hylian Maidens are the descendents of the Ancient Sages because those like Saria and Darunia were never awakened
- Master Sword still present and located in ruins deep within the Lost Woods/Sacred Grove in both ALttP and TP
LoZ/AoL—AT:
- Largely aquatic Hyrule
- Towns in this Hyrule are named after the Awakened Sages in OoT
- The Master Sword is no longer present in any way, shape, or form because it's still beneath the waves in Old Hyrule
As for OoX though, it really could take place after either ALttP or AoL due to the Triforce being restored and safekept in Hyrule Castle.
Also another point of interest.. Since the rumors circulating Zelda Wii state that Link will not be using the Master Sword and that the game has a generally more 'futuristic' feel (not meaning cyberpunk or the like, but just based after any and all of the fifteen preceding games), we really can't determine whether it takes place in the Child or Adult timelines yet. In ALttP, the Master Sword was put to rest "forever", and in WW, it was sealed within Ganondorf's head beneath the waves.
I'm going to retract the timeline I last posted and revise it here:
----------------------------------------MM → TP → ALttP[/LA] → [OoX/(LA)]
TMC → FS[/FSA] → [FSA] → OoT—{
-----------------------------------------------WW/PH → ST → LoZ/AoL[/LA] → [OoX/(LA)]
• = defined placement
• = undefined placement
I've said it before, but I'll do so again: the mere fact that FSA and OoT give Ganondorf two different backstories suggests that there are in fact two different Ganons in history. There is Trident Ganon and Triforce Ganon.
Part 1: Trident Ganon
Born prior to FSA (or FS/FSA depending on whether or not it's the same Link) as Ganondorf to the Gerudo tribe. He betrayed his people by venturing into the Pyramid and stealing the Trident of Power which incased with an ancient evil, permanently transformed him into the blue pig beast Ganon. With the Trident, he created a Dark World and began to absolve Hyrule with it. Because this Ganon did not possess the Triforce of Power for it had yet to be discovered, Link was able to defeat him with the Four Sword and seal him within it.
Part 2: Triforce Ganon
A Gerudo male is born every 100 years, so following FSA by at least 100 years, it's entirely plausible for another Ganondorf to be born prior to OoT to a later generation of the Gerudo people. He was surrogately raised by the twin witches Koume and Kotake who taught him the art of dark magic. Upon tricking Link into opening the door to the Sacred Realm by removing the Master Sword from the pedestal of time, he obtained the Triforce of Power and thus led his people on a front against Hyrule during a seven year war. After entirely usurping Hyrule, he crowned himself the new ruler of the land, watching over from atop his tower. Link, with the Master Sword, Zelda, and the Light Arrows defeated Ganondorf (who had control over transforming into Ganon unlike Trident Ganon) and with the help of the Awakened Sages sealed him within the corrupt Sacred Realm—the Dark World, though different from Trident Ganon's Dark World (which he fabricated with the use of the Trident).
Part 3: Triforce Ganon's Deaths
In the Child Timeline, Link, the Hero of Winds (WW), drove the Master Sword through Ganondorf's head, absolving him of the Triforce of Power making him mortal and thus killing him. In the Adult Timeline, Link, the Hero Chosen by the Gods (TP) killed Ganondorf by thrusting the Master Sword through his wound created by the Ancient Sages in their failed attempt to execute him. As Ganondorf and Zant seemed to share a spiritual connection, Zant's spirit seemed to sever Ganondorf's last tie to life, effectively killing him also. These are the known ends of Triforce Ganon in both timelines.
Part 4: Trident Ganon's Deaths
Since Trident Ganon arose prior to the timeline split, he too exists in both timelines, sealed within the Four Sword. Because even Vaati was able to break out of the seal, it's quite obvious that it's not a very reliable prison, especially for the likes of Ganon. This Ganon could only be killed by the Silver Arrows, a reference to such mythical beasts as werewolves who could only be killed by silver bullets and the like. Come ALttP in the CT and LoZ in the AT, both Links had to slay Trident Ganon with the Silver Arrows just as their predecessors had to slay Triforce Ganon with the Master Sword. Also since the Triforce had been discovered (whereas in FSA it had not), Trident Ganon sought the relic in both timelines. In the CT, he was originally sealed within the Four Sword in the Dark World (corrupt Sacred Realm), in the Temple of the Four Sword deep within the Pyramid of Power. After breaking free of this seal, he discovered the Triforce. ALttP's backstory about the seal war seems to be a culmination of both Triforce Ganon's story during OoT and Trident Ganon's actual presence during ALttP, mixing the two up as one entity. In the AT, Trident Ganon returns in LoZ, assuming he too broke his seal on the Four Sword. Because Triforce Ganon lost the Triforce of Power upon dying in WW, Trident Ganon must have at some point found a way to the Triforce and upon being imbalanced, received only the Triforce of Power.
Now on a last note: as for how there were Moblins in TMC, I think the most logical inference is that there was in fact another Ganon even before TMC and after his defeat, his army of Moblins were sealed within the chest by the Hero of Men.