Levels of -1 generally mean that the spell is scaling with your character level. Summons, for example, have their level set to -1 by the skill data, and in-game you see that when you're level 10, the summon is level 10 as well. The skills used by summons (and enemies) are Level -1 as well due to the fact that the summons themselves scale.
The level of the skill does correlate with the penalty, but it's also important to note that the intelligence level of the user has an impact as well. If you raise your intelligence, then the boost will increase (or become more positive) no matter what it was at before.