Storing Stormlight in gems reminds me much of how magic/mana can be stored inside of cut gems in the Eragon books (it's been a while since I read those, but I liked the concept of it). The better cut the gem, the more that it can hold. This seems to work with Stormlight too, as uncut gems can hold it, but not nearly as much or as well. In Eragon, stored mana can be sensed inside of the gems but not seen, unlike Stormlight which can be seen and not sensed, exactly.
Perhaps, somehow, the cut gems have "pockets" or "levels" in which the mana/Stormlight can be held in? It would make some sense, sort of like a building with many floors can hold a lot more people than a building with only a ground floor but a very tall ceiling. Which might be why glass, among other things, can't be used to contain Stormlight.
Being that Surgebinders breathe the stuff in, the description of it taken the form of vapor seems pretty spot on for me.