So thought to give my opinion on the whole PC, Pokeball, Poke Pelago discussion:
Poke Ball: Let's start where it all starts, the Poke Ball. The Poke Ball can turn matter into energy for storage and back into matter when opened, be it a Pokemon or item (though it seems to not affect humans. In the anime when one is thrown at a person is usually just bounces off without even opening, and the one time the beam hit a human it just stun them. Only time a "Poke Ball" affected a human was in "The Time Machine" Pokestar Studios movie where Pokemon took over and use "Human Balls", though that's just a made up movie. Still, is it just that the Poke Balls are programmed not to affect human DNA or for some reason humans are too complicated for one to be stored?). But back on track, when being stored the Pokemon still seems aware of what's happening outside and can be affected by outside changes, so they're not in your typical frozen stasis. So it could be the Poke Ball is sort of like a passenger seat of a car, the trainer being the driver. They're also being affected by time as normal, hence how they can be affected by outside changes. How this is done is iffy. Like with experience, healing, or changing a move you could theorize it's adjusting the Pokemon's energy that matches the biological process the Pokemon normally does to gain experience, heal, or learn a move. But then you have the spreading of Pokerus which would need its own theory, like does turning the biological virus into data turn it also into a digital virus that can spread via close signal connection?
Of course it has some connection to the PC. For one a Poke Ball does identify the Pokemon in it as being yours, and when you have six Pokemon with you it teleports to the PC (specifically into your PC Box).
PC: So the Poke Ball just seems to be an easy way to carry around your Pokemon and identify them as yours. So what about the PC? Pokemon do seem to be in a form of stasis while in the PC, hence why some don't change forms when they should or Pokerus doesn't go away or can't spread. Only time Pokemon are affected by the outside is when the trainer is actively using the PC, and even then what they can do is limited to moving around held items which isn't something a part of the Pokemon like moves or experience is. Now outside that we don't know what a Pokemon experiences when in the PC. Are they conscious? Does the PC create a digital environment and the Pokemon creates a digital avatar of itself while its body is in full stasis? All we do know is that Pokemon in the PC aren't affected by time, as one girl NPC noted you could deposit a Pokemon into the PC in take it out after 100 years with little to no change to it (though that brings up the question if something happens to the PC would that affect the Pokemon? Are we really releasing Pokemon or are we actually deleting them from existence?... Well, ORAS actually answered that as the Latios/Latias you make friends with will always come to with when playing the Eon Flute even if you release it).
Dream World: Let's go over the Dream World first since it came first. Aside from choosing a Pokemon from the PC, I think it's implied the Pokemon is placed in the bed connecting to Fennel's dream smoke invention. From there things get tricky, after interacting with your Pokemon's dream you can then go to a place to pick up any items you find and catch any Pokemon it befriended. At that point I would just throw it up to magic, you could at least justify the Pokemon is an actual other Pokemon who's dream just so happened to cross path with your Pokemon's so it's not like Pokemon are being created out of thin air (the items might be, but they're just objects).
Poke Pelago: So finally we get to the Poke Pelago. Since you have to fly there with Charizard Glide it does seem like a real geographical location (unlike Festival Plaza, it's confusing exactly what that is). As for how your deposited Pokemon are running around without your choice, could just be Mohn letting your Pokemon out of their Poke Ball (you essentially gave him permission to do so).
Lusamine's Collection: Lusamine put her Pokemon in cryo, a different and possibly more horrifying process. Pokemon going into the PC have been turned into energy & data via the Poke Ball, so its a smooth process with little harm being done to the Pokemon. What Lusamine did was flash freeze a Pokemon's entire body, stopping its normal body functions. While Pokemon turned into energy can easily be turned back into matter, Pokemon who underwent cryo can't just be freed from cryo. They need time to be unfrozen, and not only that but the thawing process must be done carefully as not to cause physical harm (you don't want to have an organ begin processing again without the needed bodily fluid still frozen; that will end in the organ and maybe Pokemon dying).
Type: Null/Silvally: I can only assume they didn't dispose of the Type: Null just in case they decided to start the project again if they ever discovered a possible way to get the RKS System working properly. They probably spent a lot of money on them and would just be a waste to just kill them, they were much more valuable to keep in stasis for future research purposes.
Silvally don't look to be made from any Pokemon parts I've seen. Could be they spliced together ideal subjects to create the parts they wanted for Silvally (like instead of a fin of one Water-type Pokemon, they got DNA from an ideal group of Water-types to construct its fin tail).
Here's another mystery for y'all:
Remember that scene at the very beginning of Sun and Moon? You could be excused if you didn't, many people just left the DS and let the scene run while they went to have a coffee, take a dump or do a bachelor's degree.
Anyway, it takes place on a bridge over a huge waterfall crashing down the east side of MeleMele Island. And I have to question: Where the heck does all that water come from? It's a large waterfall, with a throughput easily in the range of 10 m3/s, and a constant flow, signalling a large catchment area or a well-fed aquifer. But MeleMele Island can be circumnavigated on foot in five minutes. Worse, basic hydrology dictates that wherever it rains that much, has to lie above the waterfall. And the waterfall comes off the highest point of the island. Every other place on MeleMele (and again, you can visit them all in five minutes) lie lower than the top of the waterfall. There must be a very powerful water source somewhere up there. It can't be seawater sucked in by some trick of capillary forces, since we see vegetation in the area which would otherwise have died from the constant salt spray.
Also, why does the waterfall run down the cliffs on the east side, when the whole of MeleMele slopes to the southwest? Any natural rivers would flow the other way down the mountain and through Hau'oli City or Route 1, rather than flinging itself off the highest cliff. And nowhere do we see what happens to the rain that falls on the rest of the island, since there are no other rivers.
Great waterfall, looks dumb when you think about it.
Obviously Lana wasn't lying, there is a Kyogre living in Alola and its affecting the water flow.
Serious answer, aside "it's a game" if you want a pseudo-science explanation maybe there's some underwater tunnels which has a current which pushes water upwards where the waterfall's water supply gathers. Who knows how that works, but hey, there's also strange phenomenons in our world that goes against general laws of physics.