yup its only base abilities that count...
btw, (I haven't done this but) the $ manual suggests simply saving your skill points when you level-up (by not placing skill points into skills) and then simply shovel in those saved skill points when you reach a level where you have the skill points neccesary AND the when the level allows that many skill points for that particular skill.
For instance: I believe you can reach a skill level of 5 in stealth naturally by character level 2 regardless of class (though I'm not sure, I think that all classes allow stealth) - however if your a fighter and you have very few skill points to place into any skill at each level-up, (beyond of course character creation level 1), you might not have enough points to overcome the penalty to even place 1 skill point into steath. So instead what you do is save up the points until you reach a level where you have enough points to overcome the penalty.
Alternativly you can of course multiclass to a stealth class to overcome the penalty.
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