I'd chalk this up to one of those things that require some degree of segregation between gameplay mechanics and lore. From a storytelling perspective, it irks me that a device like a soulstone exists to shortcut the in-game "learning process". To me, it kind of cheapens a character's personal journey of self discovery. Need to learn a complex job that took generations of practitioners to master? No problem! Just pop a soulstone and, voila, you're a grandmaster!

But then again, that's just me, and as others have observed, from a strict lore perspective the soul crystals in FFXIV appear to have varying levels of efficacy, roughly corresponding with how common the jobs are. For the more "common" jobs, like paladins for example, I suspect that the soul crystals do not contain very much in the way of unique knowledge, and are really no more than just badges of identification. It appears to be a similar case for the ninja.

Then there are the extremely rare jobs like scholar, for example, where there is literally only one soul crystal of its kind left in the Seventh Astral Era (Or is there two? I can't remember whether the second scholar soul crystal discovered in the levels 60 to 70 quest line remains intact). In which case, virtually everything that the WoL Scholar knows about his job is derived from the soul crystal, and without it the job literally cannot exist today.

In short, there is no consistency to how the soul crystals work, let alone how common they actually are. Simply put, I believe we're not meant to think too hard about this.

I have a related problem with how crafting is supposed to work in FFXIV. Do crafters actually build their products through physical labour, or is it more like the way Star Trek replicators work? That is, you visualise the object in your head, you release energy from crystals, the aether reacts with your materials, and voila, you have a finished product.

In Final Fantasy 11, it was specifically stated that professional crafters build their stuff through actual labour, while adventurers use crystal synthesis to shortcut the process. It's not actually very clear in FFXIV whether that's also the case. If you go to the guild halls, you'll see crafters perpetually working on creating things. But when it comes to you yourself, the process is completely different and, more crucially, you need crystals to make it work.

I am yet to see any NPC crafter having to use crystals in order to make anything.