(Ok so I know I'm crazy at this point - you don't have to keep pointing it out.)

So get this there's the town of Clay Hill in the pilot, which is mentioned in the transport episode as no longer existing at the time that episode takes place.

When they escape the "beaten path", it also looks like just the whole outside world outside their home and surrounding area is a post-apocalyptic wasteland.

What if all the teachers are former citizens of Clay Hill seeking revenge? Or in the case of the love cult, not revenge so much as they want to convert the world's remaining survivors? The family, and the factory, also operate like cults and use similar brainwashing/gaslighting tactics to get and keep people.

Basically there was a big catastrophe. I think the truly evil teachers are ones who blame the main three specifically or want to harm them, like Lamb Chop and pals. They seem like maybe their mission is torturing the main 3 all along, but they have to pretend to be teaching something in order for their presence in the house to be "normal" for them, because they're used to the teachers showing up.

The "final boss" was kind of the transport guy, and it shows that at that point, Team Evil had perhaps run out of usable teachers.

I think Electracey, since she tells Yellow Guy about the batteries, must not be on Team Evil. I also think some characters like Warren the Eagle, might be more self-interested than purely evil. He doesn't seem like he wants to torture the main 3 or is aware that he's annoying - however a person like that could be sent by someone else, intending torture.

Roy is actually protecting them from the teachers that want to kill/enslave/trap them, shown most clearly in Family. Leslie is behind all the teachers that are evil - transport guy looking like a demon in his true form and having Leslie's name on his license plate is kind of a giveaway.

She wants revenge on the main 3 for their role in Clay Hill's destruction. She's a survivor of the incident; which also explains her scars. The incident killed her son, who reminds her of Yellow Guy just enough that she often spares him the more gruesome fates (but not always). But the main 3 are still a sore spot for her, and she seems to dislike being forced to pretend she doesn't hate them.

Roy's machine might be seen as a thing that trapped the bad teachers, or captured training data from them to use to recreate them as AIs later and shape his knowledge of how to combat them.

"my dad is... is a computer" was not just a joke, but accidentally him remembering something he's not supposed to remember (Roy is a cyborg or robot of high intelligence -he's just locked in a kind of arms race against Leslie though). Leslie keeps manipulating the situation to keep him dumb, keep him from remembering what's really going on which he's learned before. Which is that she's the evil one (he'd know if he read that book, I'm suspecting, but she uses sympathetic magic (dolls) to manipulate their behavior, and caused him to destroy it, and caused Duck to take the batteries away again).

The whole system is a mockery of education because it's set up giving the main 3 the apparent hope for an education, but keeps them trapped in a sadistic system that actively avoids teaching anything constructive, or cannot.