Where is customPHPPathDir set in 4.7.0?
I would suggest you to not use that folder anymore (Allen is detailing where you can set it), but to write extensions. 

What is usually done is to copy paste an existing php file from the core and alter it to fit your need. However, as the original file is likely to be modified in the core between versions, you will either end up with your modify version that has diverged from the core, or you'll need to apply your changes at every upgrade.

Most of what you need to be changed can usually be done more safely and robust from an extension, using hooks