That’s pretty much what I mean.
All attack skills which are [Physical] will be boosted by P.ATK and all skills which are [Magic] will be boosted by M.ATK.
If you want to know where I get this [Physical] and [Magic] from, look here.

[size=9]This is an earlier version of Heal.[/size]
All skills should mention if they’re Physical or Magical.
But some skills also get a bonus from the stat value itself.
For example, Zaibas increases directly with your INT stat value.
Because it’s a [Magic] skill, you will also have an increase in damage from your M.Atk stat.
INT does increase M.Atk, but for Zaibas, it’s like having a double bonus. You’ll get an increase in the damage of Zaibas directly from INT, as well as a bonus from M.Atk that is given by INT.
There’s a distinction from a skill ‘scaling with INT’ and a skill being affected by the bonuses from INT.
In the case of all current Wizard skills (except Summon Salamion, Summon Shoggoth and Summoning), none of them include INT in the damage calculation, but will all be boosted by M.Atk, which is a byproduct of raising INT.
Does that make sense?