I think the assessment that A&E lean heavily on anime homophobic villain tropes is spot on
for at least the first two endings.
I feel like the later endings cast that characterization in a different light.
A&E are instead an attempt by the robots to transcend themselves (robots) and the untenable situation on the Earth (perpetual conflict).* It's the Androids that are the villains and A&E are basically just emotionally children/teens, not yet grown.** Like, Adam's birth is violent and traumatic, after which you try to kill him. You essentially teach him (and by extension, Eve) violence, anger, hatred and prejudice.*** I think their story should be considered a piece with Pascal's in that they're in part about what violence and war costs the weak. (None of this gets away from the fact that they're coded as homophobic villain tropes, but my takeaway is that they didn't need to be, you made them this way and they would most likely have been kind, gentle, curious and loving [as their "parents" seemed to be]. Like, it's not a great depiction, but the underlying narrative seems to be that this isn't how people are supposed to be and it's not their fault. I'm kind of reminded of Aaron in Titus Andronicus.).
*Adam at first seems like a kind of defensive response by a group of robots you find in a city. Later endings, I think, pretty clearly indicate that he's not that at all, and is, instead, an emergency attempt by a group of robots desperately trying to find a way out of the android-robot predicament ("this cannot continue" they all proclaim). Also, on the way to these robots you encounter nonviolent robots who've modified their bodies as a kind of pacifist art, and then robots that are trying to defend their homes, robots that don't want to die, robots that cry out in pain when attacked. 2B and 9S aren't the heroes here, they're villains. In fact, the only really hopeful ending (to my mind) involves sending A&E in a ship out into space, to go somewhere else and try to find a way to live without violence.
**I think it's important to note too that Adam and Eve are the only characters in the game that particularly look and act like something from popular anime/manga (with maybe the exception of the Commander, but she's a pretty minor character): they're petulant, arch, strut around, like to go shirtless, have achingly mangaboy haircuts, angsty, one wears glasses (which must be a total affectation/fashion accessory), all of which just screams teenage boy to me.
***He's born and then stands there while you attack him. He clearly doesn't get why you're attacking him and it seems like he doesn't know how to defend himself (initially attempts at defense seem sort of an emotional response to harm, not the result of combat programming). As you attack him he gains levels and it's strongly implied that you're teaching him and what he's learning is violence (and hate). Then you appear to kill him and from his corpse is born Eve, who, clearly born with the lessons you taught Adam (especially hate and anger) takes his brother/husband and flees. No wonder Eve is always pissed off and Adam is obsessed with death. It's the first lessons you taught them.