As a single unintentional hit by either alliance can result in a low goal score, the situation described by the OP certainly can and has occurred in regional events. In my experience, the referees have called this identical scenario both as possession and not possession, depending on the context of the game and the impact on the final score. Subjective interpretations changed the outcome of many matches this weekend, up to and including elimination matches. THIS NEEDS TO CHANGE. I don't believe that any team in any sport enjoys winning by persuading a scorekeeper to their point of view (except maybe a debate team.)
Unfortunately, the game manual contains some generalized rules that fail to explicitly define the legality of specific actions (like singular incidental contact causing an opposing alliance's ball to go into a low goal.) In Aerial Assist, this puts the burden on referees to decide the winner of many matches, including regional finals. I certainly wouldn't want to be the person to tell a drive team, "After much deliberation, we have decided that you intentionally hit the wrong ball 5 minutes ago. Better luck next year!"
To answer your question, I have seen a ball scored both with or without possession, depending on the circumstance and the referees' interpretation of the rules. Because of this, I would suggest avoiding the "grey areas" of this year's rule book at all costs. This especially applies to frame extensions near the field barrier, human player fouls, and possessing an opponent's ball. Make the legality of your actions so clear that referees cannot possibly lawyer it into something against the rules. It makes life a whole lot easier for the referees and event staff and makes Aerial Assist a much more enjoyable game to play and watch.