Would it actually detect him as a Pokemon? He's immortal because of his exposure to the Ultimate Weapon, which is fueled by the life force of Pokemon and people alike. I'm not entirely sure how that immortality would work; if those lives would actually be a part of him or if their power is just keeping him alive and devoid of aging for the most part. If it's the former he might actually be detected as a Pokemon, but the likelihood of it is very low considering we don't really have any evidence he's anything more than a person infused with boundless energy that keeps him from aging and dying.
pokeballs should detect all "humans" as being pokemon, given that all the humans in the pokemon world are descended from pokemon according to the sinnoh myths + the fact that even if they had sprouted up cabbage patch kid style they would still be considered pokemon as that exactly how the weather trio & heatran came into existence.
theres to much evidence that "humans" in the pokemon world a hell of a lot more pokemon then they are human by real world standards.
other notable examples is sabrina, her father, olympia, sir arron, riley, & ash are also good examples of this given how they all got powers like that of a pokemon.
though in ash's case he needs those gloves to focus his power as he hasn't bothered to master it.
also according to sabrina(in game), all humans in that world are capable of using psychic powers.
then we also have the case of a human's turning into pokemon
It happened one morning - a boy with extrasensory powers awoke in bed transformed into Kadabra. (Kadabra FireRed Pokedex)
Each of them carries a mask that used to be its face when it was human. Sometimes they look at it and cry. (Yamask Black Pokedex)
According to old tales, these Pokémon are stumps possessed by the spirits of children who died while lost in the forest. (Phantrump Y Pokedex)
its always ghost & psychic types, so it can be theorized that humans in the pokemon world are psychic types with the occasional psychic/fighting type and turn into ghost pokemon when they die if they don't pass on.
the differences between them and the fact that despite marriages in the past there are not any hybrid roaming around can be explained by how the breeding system works given the offspring will always be the lowest on the evolutionary line of the female unless a certain item is needed(like pikachu needing a light ball to breed pichus)
as for why humans all look different can be explained by spindas
The chances of two Spinda having identical spot patterns is less than one in four billion. (Spinda Heartgold Soulsilver Pokedex)
I think that would depend on whether Xerneas's energy was used when he was exposed to it. Xerneas has been stated to be able to bestow immortality with its horns, and I think it was this power that AZ used to bring his Floette back to life before he turned his weapon on the warring factions that took its life. If he was exposed to that particular power then I'm not sure it would run out.
it might also depend upon what pokemon where sacrificed as most of the legends seem to be biologically immortal.
in fact, i'm pretty sure thats what AZ is: biologically immortal.
its also indicated by the fact that he's still aging & growing despite gaining immortality. obviously his growth slowed down at some point otherwise he's be able to easily man-handle that giant tentacruel