You learn the ability, which lets you use it freely without having to have that piece of armor equipped anymore. You can upgrade past that. However, you are still limited by how many crystal slots you have. If you have 18 crystals total, and have equipped abilities up to 16/18, and "Steal Gil" requires 4 crystals, you can't use it. It's a way to balance it so you can't eventually just be using every single ability in the game.
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