From what I understand, if an item says lethality or magic penetration and is a flat number then it will reduce the targets respective resist by that amount. Lethality is a bit different because it scales with level, but say you have 30 magic pen, and the target has 29 magic resist, that target will be treated as if they have -1 magic resist and will then take true damage from your spells. It used to be possible to get 56 mpen which was higher than the base MR of most champs at even level 18 so going full pen was very strong. Nowadays MR growth is higher and you can get at most like 40 mpen including buffs from runes that are temporary.
The general idea is flat pen for lower resist targets and percentage for all others. Black Cleaver is different because it reduces your armor so all people hitting that target will gain penetration in a manner of speaking.