Up to the tournament director. Most places by me make it so players plunge off their extra balls. I try to switch all my games into tournament mode as to not have that be an issue, but if you're not able to then plunging off is a reasonable alternative.

We turn extra balls off if we can. If we can't or a machine gets missed when we are turning them off our rule is to play it. This is common for all but one league I am a part of. The one league leaves them on and the rule is play it if you get it (this is unfair IMO but it's not my league). We also try to turn on tournament mode if possible so that all mystery awards are equal for all players.

Most places disable in settings or plunge

for the route places where I do tourneys we just have a rule of "plunge only for EBs"

You are allowed to set a lane prior to plunge but as soon as you lunge then no flipper button may be pressed.

Totally up to you. In the league I ran, we just plunged extra balls. You could plunge for a skill shot but no contact after the plunge. We did this because the games were on location and we had to let the public play on them.

For tournaments, I always try to disable extra balls if there is a setting to do so. For older games and EMs I'll often allow the extra ball and they do that at Pinburgh, too.

Other things to do are setting the games to tournament mode or using another option to make awards non-random. Also games with long ball times like LOTR and Fun house, etc. may benefit from widening outlines and removing post rubbers.