Can my iPad Pro 12.9-inch 2nd generation be modified to use the Apple Pencil (2nd generation)?

No. The iPad uses totally different hardware for pairing/charging the two versions of Apple Pencil.

No iPad can be modified from its original hardware configuration.

No.

Apple Pencil (2nd generation)

You can use Apple Pencil (2nd generation) with these iPad models: 

• iPad Pro 12.9-inch (3rd generation) and later
• iPad Pro 11-inch (1st generation) and later

You need Apple Pencil (1st generation) for your iPad Pro 12.9" 2nd generation.