I don't know if there is any good reason to truly say the Destroyer couldn't be transfigured. There isn't any scene you can point to in order to suggest it could withstand it. I know this is a gauntlet, but as the first person officially on the gauntlet can easily defeat him I will just discuss each fight.
Voldemort gets blitzed by Quicksilver easily. I think he could take the 2005 version of Doom. Hard to say if the death curse would work, but transfiguration would. Darth Vader...probably a quickdraw there. Transfiguration, fire, the death curse...all options. Even if one wanted to say the AK wouldn't kill Vader it would still most likely do some damage to his suit.
He loses to Green Lantern. The movie was terrible, but GL was pretty powerful. He has decent shields and far more overall offensive power than Voldemort. Doomsday is hard to say. Technically, just like the Destroyer, I don't think DD has any feats in the movie to suggest he could resist mystical transfiguration. That is about the only thing that would end up stopping DD.
Doctor Manhattan can win pretty easily. I don't see the death curse working on an energy being. Plus since he has enough control over his molecular structure to easily rebuild his entire body within minutes...I don't think transfiguration would do much either. DM vaporizes Voldemort.