DY: “Except that, as you noted in your letter, a siman after the fact, especially on packaging, is ineffectual.”
You are confusing two different sugyos. Milchig bread requires a Siman prior to the baking, and the Hechsher’s symbol iineffectiveve. however, here the issue is being mevatel milk to eat with meat, and practically speaking noone will eat Thomas English Muffins with meat due to the OU-D designation. Hence, there is no bitul issur.