I don't particularly like the idea of glyph-based magic either, but it's the way PS has decided to go. It does create a certain void in places, as you can't, for example, have any sort of innate spell or magic. Likewise, you cannot have magical anything, since that anything either needs to have an embedded glyph to power it (which isn't all that problematic since glyphs are readily available and can FAIK be copied as well, or at least transferred), or be powered by a spell being held active elsewhere, but that may be a particularity and not necessarily a drawback, as other magic systems are much more limited (D&D, for example).
Regardless of that, my view of how glyphs work is that they do not contain a spell, they contain a certain pattern in which the raw magic from the crystal is being channeled into the realm. When one uses a glyph, one uses it's pattern to channel magic into some effect, but the effect itself must still be determined by the caster, and the energy flowing from the glyph must be controlled and given additional shaping to actually yield the desired effect. Naturally, each glyph has a spell, or set of spells, that it lends itself to easily. With additional wisdom and experience, a caster can exert greater control over the energy output, fine-tune it, and at some point even tune it to yield different results (even though the general category remains the same, so one can't make a water glyph cast fire spells; at least it would require an exceptional degree of profession to work at all, and even more to become effective, certainly more than "just" mastering all magic ways, so it would possibly be something academic without any real-life use). At greater degrees of knowledge and experience, one can combine different glyphs (or possibly more than just one of each kind) to create further diverse spells, or to gain more raw power for the simpler spells (more than 100% power maybe, if that relates to the power handling capacity of a single glyph?). In order to synchronise these, it clearly takes more knowledge and experience, so indeed one is actually learning something when levelling through the magic ways.
Lastly, I do not think that the races would necessarily or even likely have had any sort of magic before arriving in Yliakum (that was ages ago, so it would hardly matter in Yliakum today). Since the crystal is the source of all magic, upon leaving it's vincinity (maybe not the stone labyrinths, but possibly the planetary surface), the glyphs would become powerless and maybe even vanish if they're powered by magic themselves. What does make sense is to give the, or at least some, races a certain "knack" towards some spells (or rather effects / areas of magic), which however is, at least in part, already in the race descriptions.
This could be used to make some such "last resort" spell (by way of an amulet containing a glyph, plus the very specialised training in the use of this one glyph to the greatest effect (including the ability to channel all remaining mana (plus maybe a bit more, as it's not "general purpose" mana) through it)), with the described aftereffects due to the mental stress. This wouldn't necessarily be race-bound (though the kind of spell likely would), and nowhere near everyone would possess it.
Additionally, even though this is quite a stretch, one could imagine transferring a glyph onto oneself, possibly even as a sort of birth rite, which would make for similar effects. Maybe, however, glyphs can only be transferred to lifeless objects, and I imagine that only very few (or just one) can be fit onto one single object.
