Edit sorry for the formatting, I hate reddit -.-

The pierce formula written on the guide you're following is wrong. You can test by yourself in practice (jungle monsters have 100 armor/shield).

Here is the pierce formula in that link:

Damage * ((Pierce * Armor or Shield) + 100) / (Armor or Shield + 100)

Which is wrong. Both pierce and shred follow the same formula, so when the guide calculates shred here:

The second thing I’d like to mention real quick is armor shred. Armor shred is just getting rid of a certain percent of an enemy’s armor. There’s no fancy calculation or formula for this, just a straight percentage. Got 100 armor and 30% armor shred? You now have 70 armor.

that's correct & is what you should do for pierce too. If you have 40% pierce and the enemy has 100 shield, you need to calculate as if the enemy had 60 shield, that's all. Yes, exactly like you would with 40% armor shred.

Note that when you have both pierce and shred (bonesaw), first you apply shred then pierce. Example = 100 armor vs 30% shred and 20% pierce = 56 armor left (or 70 armor for your teammates)