Diseases, poisons, spells, and other abilities can all deal damage directly to your ability scores. This damage does not actually reduce an ability, but it does apply a penalty to the skills and statistics that are based on that ability....
While in effect, these penalties function just like ability damage
Damage doesn't actually reduce your ability score, neither do penalties.Not that it makes a material difference, but it is worth noting that Atavistic Splinter applies penalties - is does not damage the ability scores.
Damage and penalties apply based on the amount of damage you take. It's an easily overlooked rule, but if you have, say, 16 strength and you take 1 ability damage - it has no effect. Your strength isn't 15 and the damage penalties only apply for every 2 points you take.
And you really don't need such a contrived and overpowered example to understand the interaction of damage and drain.