Yes,It's standard procedure to crimp the grounds together and land them in the box that contains a non I.G. device or a splice. In using the dictionary definition below, the wording in the NEC commentary is correct. Both systems can still be referred to as functionally independent even though they are connected. I now know that independent does not necessarily mean separate. Live and learn huh!!
Independent: Not dependent on anything else for function, validity, etc.; separate two independent units make up this sofa