But he does understand enough to know that potential contractees respond negatively to knowing the true nature of soul gems and the true origins of witches, and does his best to withhold that information. The history lesson and the talk about entropy both came after Madoka had already learned those horrible truths in a attempt to recast his horrible actions as something positive, and possibly to make her think that if she tried something clever like wishing the Incubators never existed, humanity would suffer as well. For someone who doesn't understand human emotions, he's pretty good at manipulating people, and knows how to avoid saying things that will discourage them.
Mm, that's not entirely true, that first point. He doesn't really do anything to withhold the information so much as doesn't provide it. If the truth comes out he doesn't act to suppress it at all, from what we've seen. When Madoka asks him if it's true, he goes "lol yea."
You're right that he gave those speeches to try to salvage Madoka's losing faith in his deal, but his timing matters. He waits to do it when the deadline for Walpurgis is almost upon her (else he could have done it before Sayaka's funeral, or whatever).
He drops those speeches because he's trying to appeal to her sense of morality and her need to be useful, things he understands to some degree. In a Potentialbomb scenario, he can still give her those talks, but the thesis is that he decided to inform her of the Potentialbomb either because A) Homura wasn't letting him talk to her through use of Desert Eagle and was planning to use Madoka to deliver it, or B) He was deliberately trying to use it to make Madoka contract with the thought of "If I tell Madoka the loops are hurting Homura, she'll make a wish to make the loops stop."
He demonstrably doesn't understand Madoka's talent for rules-lawyering or the way her sense of kindness actually works.
And from the unemotional perspective, isn't telling her that Homura has done all this for her basically telling her that Homura is an ally? Doesn't that make her more likely to listen to Homura and align with her goals? Possibly start asking her some questions about the bad things that happened in previous loops that will make the risk/reward calculation on contracting even worse? If she knows that somebody came back in time from the future a hundred times to stop her from doing something, wouldn't most people take that a sign that they should reconsider?
Madoka already knew Homura was an ally at that point in canon. Hell, she had absolute faith in Homura since before Mami died, as she personally witnessed Homura trying to spare Mami from being killed and was the only person in the series to have that context of her character.
As for the 'what if she asks questions' thing...well, see Sub-Thesis A above.
And again, if Madoka knew about the potentialbomb, why did she make such a vague wish? When she knew about the threat of witches, she crafted her wish very carefully to neutralize that threat. She's pretty good at rules-lawyering when she actually knows the rules. If she knows about the loops and her rising potential, then why didn't she try something like, "I wish that Homura's next attempt would be a complete success" or "I wish that I'd never had a high potential"? Wishing for an undetermined deus ex machina to arise to fix things sounds like something said in desperation because she didn't know enough to form a workable solution on her own.
Because both of those wish examples are fucking terrible and the wish she made was pretty much a perfect Path to Victory wish. She went much higher than "Homura's next attempt at looping" or even just "The Mitakihara situation." She made a wish with possibly as much scope as the Law of Cycles wish, and in a way that would leave Homura satisfied if it comes to pass.
Imagine, if you will. Madoka wants to help Homura. Needs to help her. She has all the information she had before, plus the Potentialbomb. She wants to fix this whole stupid system, save everyone she knows, and give Homura success.
The last one is a stickler. If she contracts, Homura automatically fails and has to try again. But maybe she accounts for that. Maybe she specifically wanted to have her cake and eat it too, planning for things to be fixed next time without her direct involvement.
But she doesn't really have THAT much time to Rules-Lawyer things out, and honestly, she doesn't need to. Wording doesn't matter.
Only intent.
And there's really only one way to get everything she wants in a single statement.
She wants everything to be fixed. The method doesn't matter; if the end result isn't what she likes, the process wouldn't produce it. She wished for a specific end state and bound all of causality, everywhere, to bend towards realizing it.
Her wish, like the one in canon, was
perfect. And the fact that it's a wish
designed to keep her from being contracted implies she knows what contracting does to Homura, because it's part of the effect and thus
part of her intent.
Hell, with that reasoning, she almost HAD to be Potentialbombed. It's the most logical explanation.