Which is more correct for the the Imam to say to the congregants when straightening the rows: "May Allah have mercy on you (all)" or "May Allah have had mercy on you (all)"?

The phrase "May Allah have mercy on you" is a supplication and not an answer to a command. It is preferable for it to be in the past tense, or in the present tense for continuity and supplication, because the order of obtaining mercy based on straightening the rows is a matter of the unseen for which there is no evidence. Rather, the Imam asks to straighten the rows and then asks Allah for mercy for them. Supplicating with both the past and present tenses is permissible.