I suppose it would make sense if ALttP came before LoZ because of its name and all, and sense the manual supposidly states it. At least that makes things a little better. But I can agree that the older games were made without regard to any others we have now. If anything, the new ones should...
I must have missed the part where the manual stated LoZ came after ALttP. Which manual are you referring to anyway?
Plus, Ganondorf (human) was the main antagonist of OoT's Child timeline. There is the point where he is not in his pig form, which I will call Ganon. He didn't become Ganon...
Wind Waker makes many references to Ganon's pig form, both in the intro story, where he is shown crawling out of his confinds or seal from wherever the sages put him, and whenever you face Puppet Ganon.
Therefore, you also have to take into consideration that Ganondorf has the knowledge of...