So, there is a lot of speculation in this thread about who goes into which pod. It seems nonsensical to me, because I'm convinced that no one will use any of the pods, other than perhaps the Darkness going to the future in one. Here is why:
First, we have the problem of getting from the data world into the real one. One of the secret reports says about this, "We're talking about the same trick that allowed the Dandelions to transfer to other worldlines after the Keyblade War." This trick cannot be the pods, because the union leaders didn't know what they are for until Maleficent told it to Lauriam. Also, would they leave the regular Dandelions at the mercy of darkness? That's not how these kids work! And then there is Elrena, whose existence in the modern timeline tells us that at least some of the regular Dandelions survived.
How about the time travel? The Master of Masters did explain away one of the problems with using the pods, namely how the time travellers get their bodies back. But the amnesia they are suffering from is still unexplained. Also, there are a lot of clues that Quadratum is somehow involved in this. We know from Melody of Memory that the leaders went there at some point. We know that the Master of Masters travelled to the future in some other way than using the pods (because no pods were missing), the description of his disappearance is quite similar to what happened to Sora, and at the end he is in Quadratum. Luxord being there also suggests a connection between it and the Dandelions, as does the stuff about dreams or visions (the ones seen in DR connect to the leaders, and Riku's ones to Quadratum). I have posted a lot about the evidence of Yozora being Ephemer before. In his character file, Luxu rambles about time going slowly or even stopping. Finally, Sora has been missing for a full year, but it doesn't look like he himself has experienced that much time. The explanation for all this is that time goes very slowly in Quadratum, therefore simply being in there is a way to go to the future of the more normal worlds, and it is also the method the union leaders used.
Then there is this chain of connections, which requires that the pods were not used in UX timeline:
The clock tower is a symbol of determinism and therefore the Master's plan. It being upside down under water means things didn't go as planned. Brain is the virus who derailed the plan, therefore it makes sense that he is also responsible for what happened to the clockwork (and this is something I should have seen much earlier than I did). Brain also has the Book and therefore the power to do such a thing on his own. And now we know his motive: the last pod being used would cause the world to fall into darkness. If the pods are under water, no-one can use them, and the fall doesn't happen.
We can continue this into the modern timeline as well. There, Xehanort has a similar machine, and there is evidence of time travel, such as Eraqus having jumped forward by something like 30-35 years between DR and BBS. Also, Scala ad Caelum got abandoned at some point. So, what if the people there found the machine (perhaps with some help from a black-coated figure) and experimented with it, not knowing about the danger associated with it. Scala fell into darkness, and its inhabitants fled to Radiant Garden. Then Scala got restored with other worlds in the aftermath of KH1, empty like we see it in KH3. This would solve so many mysteries at once!