Penalties to Abilities
 

I'm curious why penalties are applied the way they are in HL. Based upon everything I read in the rules, they are applied in applied in the same manner as ability damage, affecting the ability modifier only. Yet HL treats them as actual score adjustments. This would mean that certain aspects of the character would change and prevent them from being used. Applying the penalty the way HL does also affects other ability-based features of the character (bonus spells, number of uses per day, etc.). These numbers shouldn't be affected.

For example in HL, a character with 13 Strength becoming fatigued would no longer have access to his Power Attack feat (shows red after applying fatigue condition). Rules are the fatigue penalty would only affect the ability modifier (+1 would be come +0).

Also, HL doesn't have the adjustment to apply a "penalty" per se, only adjustments to abilities as permanent and temporary. Creating a new adjustment that applies a -4 penalty to Strength (no damage), would that be a temporary change or a permanent change? Rules make it temporary, and HL applies this as permanent in the same manner as drain.

Fatigue gives a -2 penalty to Strength and Dexterity, so your ability score is reduced, so you lose access to any things which require a higher score than your current score.

The penalty from fatigue is reducing your actual ability score, like an ability drain - it is not the same as ability damage, which only reduces the ability bonus.

Adjustments are available for "ability score damage" and "ability score drain", which apply the rules accordingly.

I don't think the Pathfinder rules differ in this context between temporary and permanent changes to ability scores.

Another example...

An alchemist's Strength mutagen applies a +4 Strength bonus and a -2 Intelligence penalty. HL does not have this as an option in the In-Play tab (including Shadow's add-on). So, is the Intelligence penalty applied as damage or drain? Applying this as a drain would affect the alchemist's number of bombs, bomb damage, and bonus extracts. Does applying the mutagen to Strength effectively make the alchemist other abilities weaker? Seems unbalanced when this doesn't happen with selecting Dexterity or Consitution with the mutagen.

Thus, why I wonder why HL is calculating ability penalties (not damage or drain) the way it does, my original question.

(I'll be submitting a ticket regarding the lack of mutagen option in the In-Play tab)

To add, the pertinent quotes from the CRB glossary under Ability damage, drain etc... are:

Some spells and abilities cause you to take an ability penalty for a limited amount of time. While in effect, these penalties function just like ability damage, but they cannot cause you to fall unconscious or die. In essence, penalties cannot decrease your ability score to less than 1.

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