Book Two of Infinity Train constructs the passenger-denizen relationship as a metaphor for gender essentialism, in a form that especially reminded me of complementarianism.
To briefly explain my layperson's understanding of complementarianism: this is a theological/spiritual belief (I'm only familiar with it existing in fundamentalist Christianity, though it could exist in other religions) that men and women were created with fundamentally different natures because they are intended for different divine purposes. You see, it is the feminists who are truly anti-woman, because they think it is demeaning for a woman to be owned like property by her father or husband for her entire life, when actually that is God's sacred purpose for all women.
Although this exact formulation of gender relations is pretty extreme, and I think the actual beliefs are more specific and elaborate than I'm describing them here, a lot of the basic premises of complementarianism are widespread. Ideas like: At birth, everyone is assigned one of two genders, which corresponds to a fundamental existential difference in who they are and which traits are the most admirable/aspirational for them. In a romantic and/or marital partnership, there is a certain role for the man and a certain role for the woman. Men exist to do things and women exist to help them.
From The Black Market Car:
One-One: But always remember there are lots of denizens along the way to help you on your journey.
Simon: You two are only as good as you are useful.
One-One: You're exactly where you're supposed to be. [...] No, you'll stay and keep helping. You're so good at it.
Can you see it? It's the idea that denizens, and Lake specifically, are supposed to be helpful to passengers. It keeps coming up over and over. Something that didn't even exist for Lake until they befriended Jesse - like because the two have a relationship with each other, Lake is suddenly defined in terms of relation to him, in a way that is deeply dehumanizing and opposed to the actual real bond the two of them share that exists outside of the passenger/denizen false dichotomy.
Marcel: One person guides. One person follows. It's a system. It's great.
This is the part that reads the strongest to me as about complementarianism specifically rather than just gender essentialism in general.
Randall: Passengers get preferential treatment because they have a greater need to exit the car.
Jesse and Grace automatically getting more points than Lake at the fair is a super obvious reference to the wage gap, especially since One-One specifically brings up the wage gap later. I think Randall's comment here is a reference to the idea of the breadwinner - the conceptualization of the husband as needing to earn a wage that can support their entire household while the wife takes care of the kids.
I think it's pretty obvious how the gender essentialism interpretation of the passenger/denizen stuff lends itself to queer readings of Lake's character arc, and especially a trans/nonbinary reading. I mean, this season isn't about Lake being like "I hate the expectations that are put on me as a denizen", it's about them literally not being a denizen and literally escaping from the denizen/passenger relationship forever.