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No, everything isn't handled by scripts. For example, I don't think the computation of the general spell DC is handled by a script; or when I have implemented the fractional BAB, I couldn't access to the script which compute BAB, since it's not a script.
eg: I have a special huserule to prevent multiclassed character to have too many class skill (I'm trying this house rule in Pathfinder, because a class skill gives you a high flat bonus to the skill: only 1 level as rogue gives you too much skill bonus everywhere). The houserule is, each time you gains a level, a fixed number of skills becomes class skills (you chose which of them from your class skill list; the number of class skill you gain is high enough to allow you to have all skill from the list after a few level - but not after only one level).
For now, I didn't use this houserule for NPC. Creating NPC is tedious enough without that. With hero lab, I could integrate this feature automatically... But I can't think about any existing Thing which looks like that. I'd have to rewrite every classes, without class skills, and with a special power which add class skills every level. I don't think I will implement that. x)
Or, I could change the way the class skill are handled by the main routine. Or, more accurately, look at the way they are handled, and try to create a mechanic which interfere with this part of the routine, in order to give the result I want without changing the classes.
(Or I can wait for a "class variant" tab if it should be available in a near future... But it should be easier to add this as part of the main mechanic)
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