Because, you know.
At the time, it was an incalculable strategic asset to the side of the righteous during the War Against The Fallen.
After the war, when...someone...was putting together the current Rakurai array, you'd need *something* to build the secondary defense platforms, and manufacture reloads (and smelt raw materials for same from somewhere?), and keep the entire contrivance maintained and operational (and fueled?) for the ensuing centuries.
A last-generation Federation industrial ship would be just the ticket for that, especially one with milspec stealth systems and a full suite of AI loyal to the chief administrator of Operation Ark.
And we know it was still there a few hours before the Alexandria Enclave died, because Word of RFC is that the weapon Langhorne used for that was concealed inside one of the ship's industrial modules until that point.
It would also explain how they built the Temple. From the gestalt impression of the text when Nimue first beheld the Temple, I infer that a small planetary manufactory such as the one under the Mountains of Light could not have done the job. It sure wasn't built by the terraforming crews.
