Here's what confuses people: It's not even a straight up spoof film
Obviously it isn't a straight Rom Com, but is also isn't just a straight parody of rom coms. It's actually a parody of parodies, within a rom con parody. It's like Parodyception. The jokes are TRYING to be awful, because the real joke is making fun of mainstream comedy.
Most people are used to regular parodies, which simply take one thing an spoof it, which is only going one spoof level "deep". Yes there are these sorts of jokes in They Came Together, but Wain also takes familiar jokes and spoofs those, by pushing them into the absurd until they shouldn't be funny anymore, but that's precisely what makes it funny. People take the jokes in this movie too "seriously"/literally. Ironic sounding, but true. You have to already be in on the overarching joke to in order to get it.