Yes, but once you do the transfer and upgrade, both "licenses" (if you even keep the Wii version after the upgrade? we don't know yet) are locked to the same system. So the Wii version becomes literally useless, and hence you did, indeed, pay more for one version of the game.
If you got to keep the Wii version and, say, put it back on your Wii to have it on another system afterward, i would understand. Heck, if they were charging you FULL PRICE while still letting you keep the Wii version on another machine I would understand (technically that's possible, if you never transfer, but then you can't transfer anything ELSE you might want from your Wii). But that's not the case, here.