uneeq: the Tzemach Tzedek would not be an issue here. His sole problem is because wine is gnerally consumed with Fleishigs, so adding minute quantities of milk would be Bittul Issur. Once the OU adds “D” to the label of the the muffins, it is no longer likely that a frum Jew would eat them with meat, and there is no issue of Bittul Issur.
BTW, Thomas is owned by Entenman’s, which I suspect is Jewish owned.