Well, with Merlin it's that basically the entire show is about the Arthur/Merlin relationship, and the fact that Merlin has to hide his true nature from Arthur, not because Arthur would necessarily want to reject him for it, but because he would have to according to the rules of his society. You can watch the show without being aware of the Merlin/Arthur subtext, but that's like reading Kafka's Metamorphosis as a story about a guy who turns into a bug, without making the connections to Kafka's own life. In doing that, you're basically only getting half the story.

With Vincent and the Doctor, the subtext was a take-it-or-leave-it thing. Seeing the subtext wasn't a moment of, "oh, so that's what this story is about", it was more a moment of "oh look, that could be fun to explore". The former would have been a form of queer representation, the latter wasn't.