I know a lot of lore-hounds would really like to see an explanation of the Wizard's Tower, but I love the idea that there are some things in the game that we'll never know. This one seems like a perfect candidate to leave alone as I doubt that any official explanation will end up being as interesting as reading (or hearing) players speculate about what it might be. (Plus: also a fun source of potential memes.)
added: I updated the title to emphasize the idea of "intended versus unintended" mysteries; the Wizard's Tower is just an infamous example.
"Face the facts. Then act on them. It's ...the only doctrine I have to offer you, & it's harder than you'd think, because I swear humans seem hardwired to do anything but. Face the facts. Don't pray, don't wish, ...FACE THE FACTS. THEN act." — Quellcrist Falconer