I live in an apartment also. Troy is outdoor trained and it is a pain to let him out when it's cold or rainy.In such an instance we have a potty pad available to him and i let him do his buisness on the balcony.
When its sunny, my daughter takes him out. It's one of those incentives of having a kid.
Automatic Dog Walker.
As for the deposit it is normal to have some pet deposit or pet rent. I pay an extra $20/month for a pet and our deposit was $250 and it's non-refundable. I would say that it is a tad odd that you have to pay for flea treatment to the carpet and cleaning after you move. That should already be done when you leave anyway. You're pet deposit should cover that at least.