@schweiz: if you add the game to steam you'll be able to use both overlays. I've tested this personally. The only thing you might miss is the shared achievements and (perhaps) shared gametime.
Speaking of which. Maybe there is a way to merge the accounts or log into the game using steam account and stardock serial.
@parrotmath: I believe that handing out steam key and immediately invalidating the stardock one would prevent the problem you describe. You don't need any kind of account to play offline. The power of having legitimate game lies in frequency of patches.
Speaking of reduced Stardock income I'd be willing to pay for the difference to migrate my copy to steam. Call it handling fee.