Magento 1 - Mage::getModel('catalog/product_website')->addProducts() not working in all cases

we are using a script to identify products missing from a website and programmatically adding them by using Mage::getModel('catalog/product_website')->addProducts(). This works in most cases, but not all.

When diving into the catalog edit screen we can see, when we do this via the GUI that a new option appears, see the image below

So the question(s) are as follows

1. Does Mage::getModel('catalog/product_website')->addProducts() return true/false upon success because now it seems when using this code all is well, but rather it is not
2. How can we circumvent this and still use addProducts() and tell it to use default values?
3. Out of interest. How/why is this question/option appearing, did we create the products not on default value level? or is at least 1 value different on some store view?