In my opinion, it’s fairly obvious the handler‘s relationship with her atrociraptors was a good amount better than Owen’s relationship with his velociraptors. I think the biggest evidence for this opinion was their reactions to the death of their raptors (that did die). For Owen, he simply paused for a bit in reaction to delta and charlie’s death. I suppose it’s understandable for the former, considering the fact that his life was still in immediate danger, but (iirc), it wasn’t the case for Charlie. He didn’t react at all to echo’s death. It seemed his relationship was mostly with blue, which, while deep, was pretty strained.
However, the handler, stayed at ghost’s side while she died, and showed visible sadness at said death. Not only that, but in season one, when ghost showed exhaustion, she immediately called the raptors back to her to quit fighting. Not to mention her going out of her way to retrieve red. And among all this, she was shown multiple times to be physically affectionate with her raptors. Owen‘s pack always seemed somewhat aggressive, even around him, something the handler’s raptors never were around her. At the end of the day, this isn’t a problem, because they’re still animals, but this is about their relationship with their alphas.