Having the option to use Vigor in some spells

Oh, okay then, that sounds really awesome. Have you tested the "physical damage" box on the spell list in usME? I'm assuming they will take the physical damage formula, but since yours it's the same of the magic one, it overall works as if it was using the Vigor valor instead of Magic's.
I'm still not sure how does it work in vanilla that function as a whole.

Yes, spells that have the "Physical damage" bit checked will use the physical damage formula. Have a look in the spell editor in FF3usME. Physical damage is a spell property used by a few spells: Pummel, Suplex, Dispatch, Slash, Quadra Slam, Quadra Slice and Tentacle. Battle and Special are technically spells and also have the physical attribute set.

The physical property is set for certain Item usage as well, like (some) Tools or Thrown weapons. All other abilities use the magical damage formula unless they have some special way of calculating damage. Whether an attack is physical or magical affects which damage formula they will use, and how their damage is modified. For example, magical attacks are modified by Mdef. Shell, and Morph, while physical attacks are modified by Defense, Safe, Row and Defend. Which means that, if an attack ignores defense, the only difference is the damage formula used.

One important difference of the damage formulas is which stat they use to calculate damage: physical attacks use Vigor, and magical attacks use Magic. Battle Power and Spell power are just two different names for the same stat: the power of the weapon/spell used. In vanilla, the formulas are different. With my hack, the only difference is whether Vigor or Magic gets used. 

So yes, if you're using my hack, you may think of the "Physical damage" checkbox in FF3usME as a "use Vigor" checkbox.