That said, lets say there's a new model that explicitly excluded closed source and copyleft licenses. Well, the MIT, MPL, Apache, BSD- they all say you can't strip their licensing off.

Okay, so to get to the spirit of your question, lets say Github managed to program a model that worked using only their own code or code that was explicitly put in the public domain. If Github managed to reproduce code that wasn't in the training set, then it can't be accused of copying it. At that point the argument could be made that it independently created it.

At the same time algorithms can't be copyrighted, but implementations of an algorithm can be, so if Github was basically just spitting out an algorithm that just happened to be implemented similarly to how some other code it wasn't trained on implemented it, then I would say there was no copyright violation.