Yes, the fanbase and Nintendo themselves use the name ''Ganondorf'' to refer to his human form and ''Ganon'' to refer to his beast form for the sake of simplicity, but both the manual of ALttP and HH establish Ganon as being a mere nickname in universe. This explains why Ganon's Castle is called that instead of ''Ganondorf's Castle'' in OoT despite him not having transformed himself yet and why Phantom Ganon is called that in the same game despite being a phantom of his human form instead of ''Phantom Ganondorf''. In TWW for example, he's interchangeably called Ganondorf and Ganon despite only remaining in human form for the entire game.
Why does it matter if ''revival/ressurection'' are used interchangeably? That goes back to the example above with people in TWW going back and forth between the names Ganondorf and Ganon being used for the same person in TWW. Synonyms exist. Reincarnation is only used once in both timelines, to refer to FSA Ganon.
Like I said it's your choice as to how you distinguish the character. However it matters because names and titles determine outcomes. If someone says that Link killed Ganondorf in OoT then they'd tell a lie. While Ganon is killed by Link and by extension Ganondorf dies, if Link had killed Ganondorf before he transformed into Ganon then it would be a timeline that never existed because the sages would never have to seal Ganondorf in any timeline.
It's the same situation about your statement with the Twili being the Shadow people. See, in Twilight Princess the Twilight realm is not the Shadow World. In both translations of the game Hyrule is referred to as the Shadow World. If there was a shadow invasion then it was Hyrule who invaded, which does happen in the HH timeline. That is the same timeline that has no mention of a Twilight banishment after Skyward Sword. And the same timeline that points out a successful execution of Ganondorf.
Unless you plan to write off the books as non-canon then you have to respect names, titles, forms, conceptions, placements, and even pictures. You were pretty spot on for most things but you misspoke for Zelda I ZE/HH. Ganon, The King of Evil and The King of Evil, Ganon are two different Ganons in the downfall timeline. The Seven sages Seal the latter but the former is exterminated. This means that the latter returns from his seal in the ZE timeline downfall split. In HH that never happens rather it's one Ganon that keeps resurrecting over and over until it's prevented in Zelda II.
EDIT: Looking back at ZE, Zelda I refers to Ganon so I'm going to respect the nomenclature. It seems that Ganon returns from his seal in the adult timeline. This makes sense as to why he
returns because he was never destroyed.
@GZ Zelda
This would mean that the Ganon in A Link between Worlds is the exterminated Ganon in ZE. That should be the answer to your question. It's actually funny because ALBW is placed twice on the ZE timeline, both having different descriptions. If you look at the top right you can see the canon where Yuga revives and fuses with a dead Ganon. Whereas the bottom left placement has no mention of Yuga's revival.