I'm going to throw rule cites at you so you have something in your pocket if this comes up again.
Starting with the tree...keep in mind that you can object to a ground rule and have the umpire formulate one (10-2-3a) that does not conflict with a book rule (4-1-2.) The stated ground rule conflicts with the book in multiple ways:
For a foul ball that touches the tree, the ground rule conflicts with 2-16-1d: A foul is a batted ball: that, while on or over foul territory, touches the person of an umpire or a player or any object foreign to the natural ground. It also conflicts with 5-1-1d1: Ball becomes dead immediately when: a foul ball touches any object other than the ground or any person other than a fielder. Thus, a foul ball hitting the tree cannot be legally caught, by rule.
For a fair ball that touches the tree, we have a conflict when we piece together 2-6-1: A batted or thrown ball is in flight until it has touched the ground or some object other than a fielder, with 2-9-1: A catch is the act of a fielder in getting secure possession in his hand or glove of a live ball in flight and firmly holding it. Once it touches the tree in fair territory, it cannot be caught for an out.
There really is no ground rule necessary, because this is covered in the book. I can think of one way to get around this and have the ground around the tree designated as a media area, but then any ball that hits the tree in fair territory is a 2-base award.
As for the boxes, I'm sure as hell not allowing them to be drawn during the game unless there's a stoppage that requires it (weather delay or the like.) If they aren't drawn before the game, I will check with the home team to make sure they are or there's a reason they aren't.
If you can, report this to your state governing body. There is no reason that varsity umpires should be having these problems.