% Stat Potentials affect base or total stat?

On chars using secondary stats to equip things, it doesn't matter what you scroll with as long as it's the best stats the item can get, since either way you're getting more points in primary stats (+20 dex or +20 luk on a thief, if your base dex goes down by 20 your base luk goes up by 20)

You are forgetting about MW, it's better to scroll for your secondary stat so you can keep it lower and benefit more from MW.