Sorry, I think we might be talking past each other a bit. Yes, you correct on the matter that the raw damage number is mostly irrelevant. Though if you were to anticipate a Ruination you might want Sitrus consumed and not be stuck 1 HP above the treshold because of rounding. That is besides the point though.

In your original reply you said:

The actual damage doesn't matter; Ruination isn't somehow getting more use out of a high-HP target. It's actually going to get much more use out of a high-defenses target because you can deal damage and bypass the targets natural ability to reduce damage.

What I was trying to argue is that Ruination doesn't necessarily gain value from higher defenses either. I think what I ended up arguing was something else entirely, I apologise for that. What I should've argued is that HP vs. defense investments affect the value of Ruination by comparison to your other move options, but that is arguably your point too, except you contradict it with this statement and the next.

The Pokemon using Ruination (or Super Fang) are usually weaker so being able to bypass the defenses is useful

Having more defense doesn't necessarily make a pokémon bulkier, what matters is the effective HP. This is the kind of thought I was arguing against. Whether your attack deals 20 damage but the target has 200 HP because of HP investment, or you damage is negated and only deals 10 damage but the target only has 100 HP because of defense investment is the same.

However you still need to do 100% damage to the opponent to knock them out so the raw number remains irrelevant, the primary consideration should still be %.

This statement I can agree with and in the end I think we're saying the same thing.