There's literally no evidence to suggest FSA Ganon is the same as any others other than his name. I think the statement about a Gerudo male being born every 100 years is a fairly big clue from Nintendo that there could be more than one Ganondorf.
The issue with that quotation is that there is generally only one Gerudo male, with the possibility of their being an overlap for a short period of time. I have checked the quotation, and the 3DS quote remains unchanged from the original:
Nabooru said:
A kid like you may not know this,
but the Gerudo race consists only
of women. Only one man is born
every hundred years...
Even though our laws say that
lone male Gerudo must become
King of the Gerudo, I'll never
bow to such an evil man!
Repeated use of words like "only" and "lone" suggest the scarcity of the event, which implies that the continuation of the Gerudo monarchy rests in the hands of Ganondorf. If Ganondorf dies, there is no remaining way to produce an heir of royal blood. This makes me skeptical of multiple Ganons because this sort of thing is harder to work around than the re-occurrence of Zelda or Link, because they don't necessarily have to share blood ties.
The Gerudo we see in FSA are a declining group, which is only fitting after the absence of a Gerudo king, which means they would have had to depart from traditional Gerudo customs and abandon the bloodline of the monarchy and make regular practice of bearing children with those outside of the Gerudo tribe. This is referenced in OoT as "searching for boyfriends," but that does not necessarily indicate child-bearing (with perhaps the exception of Talon's wife).
One thing that makes me believe Ganondorf does not die at the end of TP is that the ToP leaves his hand
after he has been stabbed with the Master Sword; we don't necessarily know the exact reason for its departure from his hand -- its departure may be tied to his defeat rather than death. If the fatality of the blow is determined by when the blow is dealt, he was "protected" under the ToP because he still had it at the time of being stabbed. We know that TWW Ganondorf died without the ToP in his hand -- it had left to form the full Triforce. Then the Master Sword was embedded in his skull, which has happened before in OoT, although Ganondorf had the ToP at the time. Perhaps it is the fact that the Master Sword remains embedded in Ganondorf that constitutes his confirmed death, because the weapon that is designed to defeat him is constantly inflicting a wound. However, unlike in TWW, the Master Sword is removed from Ganondorf's body (it can be seen returned to Link's sheath at 4:43 of this video:
http://www.youtube.com/watch?v=EmxxIZapJXc ); if the wound to his stomach was not fatal, it is possible that he could have survived unbeknownst to Link and Zelda.
At any rate, if Ganondorf does not die at the end of TP, he would become a nomadic character like the one we see in FSA. He had become estranged from the Gerudo for over 100 years, having been sealed in the Twilight Realm, and all his connections with TP characters are now defunct, because Zant is dead. It is not uncharacteristic of this same Ganondorf, whom we know from OoT to be incredibly ambitious and willing to do anything for power, that he would betray his former tribe for the prospect of regaining some of his lost power.
Four Swords Adventures said:
Once every 100 years, a
special child is born unto
my people.
That child is destined to
be the mighty guardian of
the Gerudo and the desert.
But this child, its heart
grew twisted with every
passing year.
The child became a man
who hungered for power
at any price.
Note that the word "child" is used in place of OoT's "male" in FSA, but it is not a retcon of "male" because OoT 3DS' text is the most recent game and bears the same text as the original. Child is a more ambiguous term, and does not preclude the notion that the "special child" is always male.
The description of Ganondorf in FSA matches what we know of him in OoT, so I wouldn't say there is "no evidence" at all.
