Whatever the circumstance, IMO they had just found the remains, but hadn't officially identified them. They first confronted his girlfriend with the evidence, as it was more likely she would confess and cooperate with them in getting solid evidence to arrest him. This is standard FBI procedure. The key is that the suspect shouldn't realize he's the prime suspect. This is how, for eg, they successfully prosecuted the murderer of a university student in Illinois, his girlfriend wore a wire and he walked around with her, bragging about what he'd done.
Then the news broke that remains had been found, which AR saw. AR went AWOL, that made his guilt more probable, though I think they still were pursuing him for questioning, rather than arrest. Instead, he had no confidence he would get away with it, and shot himself.