Another thought about that ending, actually: the employees can force Celestia to tell the truth, but surely they have other powers like giving orders? Do they retain the powers when uploaded? They're mentally the same person after all, and it wouldn't make sense for Celestia to try to optimize then if she's killing them when uploading. Easier to just make more NPC ponies, if that counts.

If they retain such powers, then they represent the single greatest threat to Celestia after the Rapture, and we might expect more modification. For example, Celestia might steer Lars into not just accepting being a pony - but forgetting about his human life (including his dangerous status as an employee). And was Hanna originally a lesbian? But now she really loves her little alicorn...

Also, the ordering of chapters was kind of odd. I'd put the 'celestial' view point at the very end, for example.