There are more than two portals, as each race came through their own. It is unknown exactly where the other portals are, as some of the races made long journeys through the caves. No one came from the surface.
There are two distinct portals, plus one that may or may not be the same as the one outside Yliakum. It is certain that Diaboli, Dermorians and Klyros came through portals. It is not clear if all or some portals are connected to more than one source portal, allowing more than one race to come through any given portal. However, there is no hint to where Ylians, Enkidukai, Xacha, Nolthrir, Stonebreakers or Hamerwielders came from, except from outside Yliakum, therefore there may or may not be more than two portals.
The Stonebreakers, however, might have originated on the same planet as Yliakum:
The clan of Stonebreakers have lived for centuries digging tunnels, shafts, wells and caves in the deep of earth until they arrived to Yliakum.
All races appeared in Yliakum within more or less the same time period, and "centuries" may or may not extend beyond that (depending on what "a long time" is (Laanx studying the portal)).
The reason of this coincidence is an earthquake that moved the surface of the earth creating new tunnels and caverns. After the initial fear these tunnels were explored by the inhabitants of the surface and some of them, covering a very great distance, were discovered to connect to the Stone Labyrinths that are connected to Yliakum
This seemingly contradicts
All other races are said to arrive from magical portals connected to other worlds.
However, given that the first sets forth a statement, whereas the second only declares a theory, it is possible to have both coexist: some races came from the surface, but everyone
believes they came through portals.
Given their similarities, it is likely that both dwarven races came from the same place. Likewise, Ylians and Xacha may originally have come from the same place, though there they must have been separated for
quite a while. If this is the case, then the Xacha seem to come from some region beyond the tropics.
Some old Xacha tell about a land where light was very dim and not always present
Also, the Nolthrir may have come from the same place as the Dermorians, with just a very different lifestyle, since the major alterations are attributed to the crystal.
OTOH, the clearly dissimilar races very likely originated at different places entirely, except possibly for humans / dwarves which might have the same overall origin.
Ynnwns are "native" to Yliakum in the way that they came into existance only after Diaboli mated with elves.
As to what material is immune to the Crystal's powers, you have missed an even more obvious answer. Air itself would have to be very resistant.
It is also possible that the air simply re-forms when it leaves the direct vincinity of the crystal, since the crystal just dissociates, not annihilates matter.
