How come I've never seen an umpire make a batter stay in the box or seen a pitcher violate a pitch clock.
Because you must not really be paying attention.
Can the ump award a ball or a strike for a violation?
According to the MLB rule book, yes. A pitcher has 12 seconds from the time he has the ball in his possession and the batter is in the box and alert to the pitcher, as long as no one is on base.
As for the 1- minute pitching change, I'll stand behind my suggestion 100%.
The suggestion is stupid. You can't dictate how long the coach takes to get to the mound and how long the pitcher takes to get to the mound. But, there is a rule that a pitcher has 1 minute to throw his 8 warm up tosses between innings or when being called on in relief, except in the case of an injury.
You must not really pay attention to baseball very much.