My manager has been charging a $250 flat non refundable pet fee, which seems sort of useless, in fact may even make a tenant feel like they've "paid in advance for any damage, so why be astute about animal's behavior?" 

I also had vandalism with damages for over 20k.

The roof will not get an accelerated schedule, however having a cost and square footage broken out will extremely useful in the case of damage. 

However, our quote included fixing a large water damage leak in the kitchen floor and wall, cleaning the carpet in the bedrooms since it's not bad just dirty, new vinyl plank in the common areas, light renovations on the bathrooms, new windows, new paint throughout, new hot water heater... more I can't even remember.

However, when getting the foundation repaired, it can often damage the plumbing and structure.

Both of these scenarios can do damage to the seller especially if they are counting on that money to relocate or pay for other expenses.

They cannot bring suit until the house has been sold to another party, because there are no damages yet. 

that money can go into a trust and when the tenant moves out at the end of June, if there are no damages, the seller can get the money back.

Whatever you buy, I would focus on making sure you can replace it if it gets damaged (and replace it quickly).

If so, how would I ever be able to tell if any damage was committed by them or was previous to their move in?