Sticking to the lease in this case will only cause you more problems, not less. 

The pet fee is there to take into account that there is another 'body', if you will, that is living in the property, and is thus causing more wear and tear on it. 

He can use it as much or little as he wants and it wont cause friction.

. $50+K is too much damage to not do anything especially if he is a person in a position of authority and can cause problems for others.I'm curious.

There are also other minor issues, but nothing that I foresee will cause serious livability issues.

People can't justify leaving their 4% mortgage right now this causes a little bit of a stalemate. 

Failing to budget correctly for repairs or not accounting for unexpected expenses can cause you to go over budget.

I do work remotely from the home and was also wondering if I could write off the portion of where I use the space as a office on the same home as he’s claiming without causing any flags on the property address.

A tenant should not have to pay for that unless they continually leave food out and cause more pests than your account covers.3.

One thing that OOS people don't understand is that Californians have Proposition 13 and our property taxes to up a maximum of 2% a year (unless someone does a significant renovation causing the property value to be reassessed).