It's not a wasted opportunity, was specifically stated AF gear is going to already be powerful. You meld crafted gear to make it powerful.
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Main focuses of materia melding are to make gear powerful and to customize based on your preferences.
JSE are for jobs. They will be powerful beyond everything, because they are limited to jobs. Jobs have very specific roles, and thus customization isn't a focal point in itemization.
In conclusion, there is no need beyond "welllll... I wanna do eeeeet" to meld AF gear.
welllll... I wanna do eeeeet