I'd say no on the TGEOB - It will still change to Silver for Demons and Iron for Devils and get you the Bane bonuses.
on the TGUB, its a bit less DPS on Skellies. It will no longer turn your slicing axe into a bludgeoning axe for skellies, so your damage will go down on skeletons.
Transmuting works by getting to an enemie's weakness. Some are vulnerable to silver, iron, adamantine, etc. Others are vulnerable to slicing or bludgeoning or piercing (axeblock, hammerblock or spearblock), Transmuting at the moment changes a mace to a sharp sword-like thing while still giving you the bonus for weilding a bludgeoning item that you got from your specalization feat. After Mod9, it won't change a mace to a sword or a sword to a mace or dagger.