Noob confusion about lethality/armor pen

Ok, I'm not really a noob - I just play like one. I've played League casually for a few years now, and I feel like I've never really understood the relationship between resistances and penetration. Having armor pen shift into "lethality" certainly hasn't made things less confusing.

My question is less "please explain this mechanical system to me" and more "why is this so unintuitive and can/should anything be done to improve that fact"?

The gist of my complaint is that when I hear "armor penetration" as a stat, I assume that it's going to be most effective against enemies who build/rely on armor. My current understanding is that because of the way resistance scales with diminishing returns as it's stacked, removing a flat chunk of resistance is far more impactful when the target has minimal resistance to begin with. Am I right so far? This means that %penetration items like and do fit with the noob intuition, while flat pen (or lethality) items don't. I guess this was part of the rationale for changing the name of armor pen and taking out some of the flat magic pen.

So if I've got this right, I guess my question is... why? Why have flat penetration in the game at all if its functionality is the opposite of what's intuitively expected? Does it actually make gameplay more exciting to have to build MORE armor against an assassin who stacks lethality, rather than simply building armor because it's good against what assassins inherently do? Does it make the game more interesting to do balancing-math between penetration and raw damage stats? I imagine at a certain level of mastery, the answer might be yes. But at my bronze/silver level, it just feels like a needless barrier to entry in a game that already has plenty of barriers.

I welcome any discussion on the topic, especially if you can chance my opinion/enlighten me.