I think that the point *is* to depict them as uncomfortable and unhealthy. I mean, Tamaki himself is living in a toxic environment and is pretty much traumatized because of the unhealthy relationship he has with his mother, and the manga didn't shy away from depicting it.
Also, Shii himself is still a kid, AND he had his first sexual experiences with a guy much older than him while still being a middle schooler. He was never taught about boundaries, I think it's only logical for their relationship to be uncomfortable.