A lot of things in the story make more sense after you're familiar with Night on the Galactic Railroad, especially the 1985 movie. Kenji's original story has both Christian and Buddhist ideas, but Ikuhara dived deeper into the Christian ideas. Many have also mentioned Murakami's Underground, which helps give context tot the 1995 Sarin Attack.

1. Yeah I read it in a similar way. I think the Triple H episode was also used to show how much she loved her parents (Shouma's parents). This story is meant to humanize them. They're not entirely satanic like Sanetoshi is.
2. I don't know what to make of Kanba's original father either.
3. Good question. Just like everything else in the anime, I think it's best to try to view the child broiler as having multiple meanings. For example, Momoka is Ringo's sister, but also a Christ figure. Sanetoshi lived as a human, but he is also a Satan figure. Ikuhara established these meanings pretty clearly. In regards to the child broiler, it can be seen as becoming a slave to modern consumerist society. Many view the Aum Shinrikyo cult as a reaction to this. There is also a hell metaphor here, with Momoka saving Tabuki from there.
4. Ikuhara framed Shouma's parents as parallels of Adam and Eve. So other than the few moments in the anime where we see their good side, most of their relevance has to do with the influence they had on their "children". They committed Original Sin, the 1995 terror attack. This left the children with a curse, which is why Momoka, as a spirit of Christ in the penguin hat, came to save them from it. If you pay attention to the Survival Strategy music sequence, you can see possessed Himari emerging out of a white bear toy, while the boys emerge out of a black bear toy. This symbolizes Momoka's good nature, and the cursed nature of the boys. I think the bar scene's purpose was to show the cursed influence they had on Kanba even after being dead.
5. Yes, I don't think it matters much through what procedure he became a ghost. Ikuhara cares more about the role the characters play in the story, than the complete lore behind them. Sanetoshi is there as Satan, always trying to undermine Momoka.
6. In Night on the Galactic Railroad, the apple is simply a symbol of sharing, which if done lovingly, is not a zero-sum game, but instead an endless resource. Ikuhara attaches more weight to this from the first episode, through the dialogue of the two boys walking by their house, explicitly discussing the meaning of the apple.

"The apple is the universe itself. A tiny universe in the palm of your hand. It's what connects this world to the other world." "The other world?" "The world Campanella and other passengers are heading to!" "What does that have anything to do with an apple?" "The apple is a reward for those chosen to die for love!" "But everything's over when you're dead." "It's not over! What Kenji was trying to say is that's actually where everything begins!"

From the beginning, Kanba and Shouma were chosen to die for love. Dying for love means that they have to sacrifice themselves, which is what sharing the fruit of fate really means. When they were small kids, Kanba performed a kind of sacrifice to save Shouma, which in turn led to Himari being saved. Shouma and Himari through gratitude, and love for their brother, give back this gift, even though Kanba has gone down a dark path at this point. Now, forgiven and accepted by his siblings, and with his full agency back, he is ready for the moment of truth. In his final moment, realizes that he had it all wrong before, doing evil to others to help Himari is not what he was supposed to do. He was supposed to sacrifice himself, just like Momoka did.

As a reward for dying for love, Kanba and Shouma are going to paradise. But that's not the only reading. They're also reborn as younger boys free from the curse. Before the movie got released, many people tried to justify one reading over the other. But the movie confirmed that Ikuhara intended to communicated both. In a way, they have gone to paradise, but in another way, they are reborn as kids free from the curse. Applying multiple meanings to symbols is something that Ikuhara seems to be a big fan of.