The analogy that Junior discovers between Penelope and his father is based on the particularly damaging behaviours that both of them engage in. This is when he discovers that Penelope is bulimic and she attempts to explain to Junior why that is better than being an anorexic, but she is only a bulimic when she is actually being sick, whereas, in her opinion, anorexics are anorexic all the time. This creates a moment of insight for Junior, as he realises that everybody is alike, even somebody like Penelope and somebody like his father, as everybody has pain and everybody tries different ways to make it vanish:
Penelope gorges on her pain and then throws it up and flushes it away. My dad drinks his pain away.
This is a significant moment for Junior, as it marks his realisation that even though one of the biggest defining differences in his life is the colour of his skin and his ethnicity, there are actually things that unite all humans, no matter whether they are Indian or white.