Reading through the manual, there isn’t a very clear definition on how the Autonomous Bonus is given out. Or at least, there isn’t much on the exact procedure being used. The only definition I can find is:
Is the intention that at the end of Autonomous, all pieces on the playing field are immediately assessed and tallied. Then, the Alliance with the higher of the scores will receive the bonus, and the tallies are thrown away, with only the four point bonus remaining.
I imagine that this is the procedure, but am looking for confirmation.