Turtle Natural Armor gets overridden by Armor and based on book it should not

Can you point out where in the book it says this? As I'm pretty sure says the book says that can't wear armour.

But if you want to say they can then the rule of thumb for all D&D 5e calculations is,  if it defines a new base then it doesn't stack. For example the torte sets the base armour to 17, and if you read the armour carefully, leather armour sets the base to 11 + Dex, and so does unarmoured defence monk for instance sets the base to 10 + dex + wis. So none of these would ever stack you would just take the one that gives you the highest bonus. 

In the Torle Package supplement, it says "you are ill-suited to wearing armour." So, it is not a complete impossibility to wear an armour. Discretion of the DM comes into play here.

As He_Ian, pointed out, when wearing an armour in the character sheet, the sheet reads only the armour AC calculation when technically it should read the maximum between the two.

To clarify, the tortle's Natural Armor says this:

Due to your shell and the shape of your body, you are ill-suited to wearing armor. Your shell provides ample protection, however; it gives you a base AC of 17 (your Dexterity modifier doesn’t affect this number). You gain no benefit from wearing armor, but if you are using a shield, you can apply the shield’s bonus as normal.