I don’t think all the pieces will be counted every time. For Nothing but Net, if referees could eyeball the nets and tell one had more balls than the other without counting, they could award the auto bonus based on visual alone, but they usually only did the counting if it looked too close to call. I imagine this will be the same this year.
Yes for auto they’d “throw away” the tallies. All the scores are calculated officially at the end of the match per <G10>.
The VEX Tournament Manager, as what I heard, should be updating and would include a live scoring feature. So maybe live scoring would decide the auton winner.
Most probably they would tally the autonomous winner this year, since it’s practically the only choice. One thing I would consider is hanging in autonomous for an insanely high chance of winning 
The problem with hanging in autonomous is that the points only count towards the autonomous bonus. You could score just as many points by taking three stars out of your far zone and launching them into your opponent’s far zone, descoring six points and scoring six points.