I'm not sure if King Daphnes is dead in ww. It never says that he died, but that he was sealed away along with Hyrule. It might be something similar to how Ganondorf is sealed, in a state where he doesn't really age or anything and he can still affects certain things in the outside world when his seal weakens. In that same way King Daphnes doesn't die, and he's able to exert his power over the King of the Red Lions. I don't have any confirmation on that though, it's just an idea.
''King Daphnes Nohansen Hyrule
, ordered by the gods to put an end to Ganondorf's ambitions, awoke from his slumber.
His spirit took up residence in a small red boat known as the King of Red Lions, and he began searching for the new Hero and the descendent of the royal family. --Hyrule Historia (Dark Horse Books), pg. 124''
The bold makes it clear that he's in the same state as Rhoam as in BotW; dead, but his spirit remains so that he can help the hero. Both Daphnes and Rhoam also have similar characteristics(like appearing out of nowhere, like how Daphnes does when Ganon is about to claim the Triforce or how Rhoam does when he appears on the GP Tower to Link's surprise). I doubt his body would be able to survive the sealing for hundreds of years as he's a human man, not to mention that he should appear in the flesh instead of a spirit that possesses inanimate objects and appears out of nowhere in TWW if that's the case.
As for Ganon, I mean, yes, he was born as a human man, but:
1. He became the Demon King in OoT.
2. He is in possession of the ToP.
3. Magic wielding Gerudo seem to have a long lifespan if Twinrova is to be believed; Ganondorf was capable of using magic even before becoming the Demon King in OoT(as demonstrated by him cursing the Deku Tree and shooting at Link with an energy orb after Jabu Jabu's Belly as examples).
So those factors combined give us a perfectly understandable explanation as to why Ganon wouldn't age. Daphnes doesn't have anything like that going for him.
I would also argue that ALBW Ganon's corpse still wields the Triforce of Power because it makes the ending of OoX leading to the beginning of ALBW work better (the Room of Rites being in Lorule, thus explaining why Ganon was sealed in Lorule, even though we saw him literally explode at the end of that game (but maybe he survived that???)), however, that's pretty tangential.
Ganon dies at the end of the Oracle games, and is sealed in the beginning of ALBW.
Something happened between the Oracles and ALBW. This is made clear by the fact that the story of the hero fighting Ganon in the backstory of ALBW doesn't match up with any other known event that has happened in the DT so far.
1. Ganon is sealed with the ToP in his possession. In the DT ending of OoT, he's sealed with the COMPLETE Triforce, and he dies at the end of both ALttP and the Oracles.
2. Seven Sages are awakened by the hero, not Seven Maidens like in ALttP, and unlike those and the Awakened Sages, an incarnation of Princess Zelda is not a member of them.
Ganon had to have been revived prior to ALBW, so he could be sealed; not only are there groups and people like Twinrova, the Eyes of Ganon, and the Yiga that want to revive him throughout the DT, but there is also the fact that we know that demons can eventually revive by themselves through their own malice. Ganon does it in BotW, Cursed Bokobliins are said to do this in Fi's description in SS, etc. so no matter how he is revived, we know it's inevitable, especially when you consider how big a theme it is for Ganon to revive over and over on the DT.
They don't have bodies to actually touch the Triforce with. Maybe he's like Rhoma in that he can interact with the world?
Yeah, pretty much; the fact that they both possess many of the same or similar behaviours and abilities would suggest this.
Or why did they leave the book open for the Deku Tree Theory of post-Wind Waker Hyrule?
Spirit Tracks pretty much jossed that theory, although it didn't have much going for it in the first place(a new land created by the GDT wouldn't necessarily be a New Hyrule, for one, not to mention the fact that trees expanding the land would bury everything beneath them, not somehow pull Old Hyrule up)