Ask a landlord-tenant lawyer and get answers ASAP
Yes, the Association can be held liable for the amount of rent lost.
Yes, the Tenant can withhold rent pursuant to the clause that you cited. The room is "untenantable" if the Tenant has to move her furniture out of the room when it rains. Regardless of the Association's responsibility to timely repair the leak, you are ultimately liable to your Tenant. You have a contract with the Tenant. The Tenant has no contract with the Association.
You need to direct billing questions to Customer Service. I am only a site user just like you and as such I do not have the answer to your billing question.