Ha, I just posted something extremely similar to this in the patch discussion. It's a great idea! Giving players more incentive to actually run the Clockworks means that players are running more varied levels (and potentially exploring different elevators, rather than the old days where everyone found the one that had the boss they wanted and pummelled it until it rotated out), which reduces player fatigue (it's your own fault if you're bored silly of grinding The King Of Ashes but won't stop because you're addicted to the crowns and run SK as a numbers game rather than as Fun, but still, it happens, and I can understand why).
Perhaps a way to do it would be to give, say, one level per Tier a chance to spawn one of these miniboss rooms, and tie it to the floor's monster theme - maybe even give them different tokens (so if you found a Wolver miniboss, its tokens would go towards Wolver prize boxes &c) to encourage players to explore different elevators with different level themes. As far as the bosses themselves went, I'd be perfectly happy with giant versions of extant beasties, pitched at something like Danger Room difficulty and with accompanying normal enemies.
Prize box items should probably be costumes and accessories only, in keeping with the spirit of the Dark Harvest prizes. It's a good system that prevents people laying hands on powerful gear through pure luck.
Finally, I'd suggest that the tokens dropped by these minibosses didn't expire; because the rewards would be cosmetic and the encounters themselves rotating and repeating, I think it'd be alright to allow players to stockpile them.
