Yes, you're reading the rules correctly: they can hold the space for 3 days, but the fare is not guaranteed until ticketed (i.e. if AA changes price and/or rules or withdraws it, you're SOL).
I'm assuming you're not going direct to AA (or an online agency) because of a corporate contract or such, right? Note: some agencies have a tendency of selling not what the customer needs, but what makes sense for the agency to sell...could it be a case of the agency/agent getting some $$ or free trips from JL or from whatever carrier they're trying to sell you on? Or are they just plain incompetent for their $40?