In my head, Toby's physical features would be something like this.
He looks much more like his mother, while Lyra was a mix of both. So his features were softer, even a bit androgynous, but not necessarily effeminate.
And his body and facial hair didn't develop until adulthood, as he was also hairless. And when it finally grew, it was an achievement for him.
He did have some insecurity about his prominent teeth, since during his short time in elementary school, kids would tease him about them, patronizingly calling him "rabbit." He then forgot about it once he grew up and had to be homeschooled. But it will still affect him if you mention it. It also depends on how he perceives those comments, but generally he doesn't like people talking about his teeth.
But as he grew older, he neglected his appearance even more, and along with the lack of control of his illnesses, his features deteriorated and became coarser.