The Contradiction and Possible Explanations
In Chapter 4, everyone used Harley's usefulness to justify their various choices regarding him.
Harley said he was the Prototype's only shot at catching the secret, and Prototype validated that reading.
In Chapter 5, Prototype rights, "Dr. Sawyer's cooperation is useful, if inconsequential."
In Chapter 4, Leith says, "We can't kill him Eddie [...] because like it or not, we still need him."
He says that the reason Harley is alive in the jar and not dead within Boxy is when he validates that yes he needs Harley's mind & intellect.
But then look: he puts Harley in the secondary labs: not to oversee the main research - but to simply give Bruno advice as the secondary labs euthanize and dissect "failed" experiments - aside from being yet another humiliation tool - another "You're not good enough for the Primary Labs."
But, that's not the FULL story, because the story actively shows us that Harley's transformation into Experiment 1354 caused a notable DOWNWARD TREND in experiment's success:
The game shows us all the experiments in the late 1300s, after Harley's transformation: they're all small, and they all got sent to secondary labs for salvage: these five experiments were all found in the secondary labs and we can clearly see they failed:
So Harley's transformation did cause a downgrade.
But then...Leith DOESN'T CARE????
Bruno is still head of secondary labs. Anthony, the sicko, is having an anniversary party of the day they put Harley's brain in a jar and inviting everyone.
And Leith and Eddie? They don't even care.
Eddie Ritterman: "You worry too much. Try focusing on the bigger picture: Our friends in Tokyo are coming up to speed. At this rate, this factory won't even be our main focus in a few short years."
Leith Pierre: "And the park?"
Eddie Ritterman: "Renovations are underway. I'll be inspecting the premises next week. 7th to the 12th. I trust you won't burn this place down in my absence."
Leith Pierre: "(laughs) I'll do my best. Though I won't lie, this place is feeling more like a powder keg every day."
Leith seems to at least know that things are going to pot: correctly so.
Now that I think of it this accurately reflects their characters: Eddie didn't care about killing Harley, and he is optimistic about the future of Playtime's great work: Leith is the one who is anxious. Leith is the one who senses an explosion.
As grim as this sounds, I can see Prototype simply lying to Harley about why he's still alive and using him as a scapegoat/pressure valve to vent at whenever he's frustrated.
BUT: we know Harley is genuinely brilliant. So Prototype could also be impatient.
As for Leith, The Brain Trust, and Eddie:
Eddie hasn't changed since Chapter 4. He doesn't care if Harley lives or dies. He doesn't think The Project needs Harley, and he still doesn't, chiding Leith as "worrying too much".
Leith, on the other hand, has doubts. Of course he's too much of a hardheaded jerk to go eat his words after rubbing the experimentation in Harley's face. His pride is too great for him to admit that he killed his golden goose by subjecting a deteriorating mind whose genius he wanted to harvest to immense psychological torture.
The Brain Trust Bullies, as I've taken to calling them, are similar.
I'm sure they rationalized: Like everyone else, they rationalize (badly): "Harley was annoying sometimes, so he deserves torture."
"We all did the same experiments but he was more deranged so he deserves to suffer."
"Even if his weekly check ups indicate his annoying behaviors were indicative of profound untreated psychological ailments rather then intentional malice, we still felt burdened by them so we can treat him how he liked."
This whole situation just leaves me with a lot of thoughts...
I wonder if Leith would have profited more from immortality if they didn't ever discover it.
Or if they were in the state where: they can't share it with the world yet, they have to keep the research a secret, and it's valuable that way.
Maybe that's why he doesn't care. He has Harley's BBI. He has investments. He has money. At this point, The Project isn't a money hole - it's a money fountain and he's the only one who sees it: the Brain Trust Bullies and other scientists are obsessed with the work and and their pride too focused on their dislike of Harley.
It's like Leith said in Stella Greyber Project Audit: "We're still working out a timeline."
Always the future. Never quite sure when it will happen. But it will. And until it does...we can do whatever we want to justify it. Innovation Is Key.
I think that, by Experiment 1468, even if they hadn't finished the golden path, Leith, Stella, and Eddie had gotten everything they needed.
Had everything they needed. Lily Lovebraids is a practically humanoid body, and even with individually mobile face features, even if she's hardly a perfect copy of a human. But still-
Same height, correct human proportions.
A little cartoony but not overly so. I can see Eddie putting himself in a humanoid body to avoid his disease from going any further.
And Leith? Oh, Leith, well...he had his money.
Stella could have her child's body if they were able to almost make humanoid dolls, albeit not perfectly immortal ones.
They kept saying they were going to share it with the world, but I think only the really zealous Innovation Cultists expected the research to come out...or Harley, who thought they would publish it and make him famous.