The obfuscated code is only of the trial package, purchased packages don't include any obfuscated file. Maybe you are using the trial package instead of a purchased license? after you buy a license you need to download a new package to remove trial watermarks and get access to the code of files.
The autoloader of phpdocx includes all files of the library doing a require of the CreateDocx.inc file, so you don't need to add the WordFragment.inc manually. Please check the included samples, all of them include just CreateDocx.inc to use all methods available (except MultiMerge, DocxUtilities, Crypto, DigitalSignature and the transform method that can be used standalone).