Well, since materia is essentially refined aether crystals, I would say that materia merely adjusts the aetheric properties of your weapon in a specific fashion depending on the type of materia used. Remember that your weapon is actually bound to your soul (and while this is nominally a game mechanic, the relic weapon questline makes no bones about the fact that the weapon is connected to you, personally, as a character). As such, any materia you put into it should affect yourself in some form or fashion.
Remember: when in doubt, the answer is aether. Which is just a fancy word for "magic", really, but you know...
Remember: when in doubt, the answer is aether. Which is just a fancy word for "magic", really, but you know...
