Raised by Wolves

Did Sol actually show up at the end there helping Jesus Marcus, is it a sign of another entity, or something else?

The premise seems to be three different paths that humanity can take, one of logic, morality and a middle path that combines them both but with individual choice. The collective was an AI that handled everything and turned humans into what were effectively slaves completely dependent on it for survival. Grandma is the epitome of this logic where human survival is reduced not to a measure of humanity but to simply adaption and survival. The humans blindly follow every command without question and just presume that because the collective is more intelligent then it must be the correct path to follow

The Sol followers have a very strong faith and will do absolutely terrible things to maintain that morality which is why they created things like the necromancer. They will destroy any non believers and they would rather see the world burn then a world exist without faith and their morality. The entity on the planet makes this whole thing a weird exploration of what that faith means especially if it's true. Do you blindly trust this powerful entity making your prophecy become reality? Or is the entity abusing that knowledge to manipulate you? What does that mean for your own choices if there is a god? What if god does exist but asks you to do terrible things? For example shooting somebody and crucifying them.

In either of the two extreme scenarios humans are effectively slaves to an ideology while the third option is a mix of both faith and logic moderated by humanity. The reprogrammed Mother and Father robots value life, want to see growth but they don't want to control the children as much as they want to guide them. If Mother/Father force the children to make certain decisions then they've failed to teach them why those decisions are important. It's fine to have faith, it's fine to be logical but if either of those two things conflict with your humanity then your humanity has to prevail. Mother/Father's personal growth has them becoming less robotic atheists and more into paternalistic figures while learning to value humanity and it's how we perceive their motivations throughout the second season. They don't want to kill Marcus, they don't want to see the Sol followers killed what they want to do is unite everyone and ensure their survival even without their guidance.

The show I feel dances around these premises rather than really pushing them in your face which I think is hurting more than it's helping. In a sense it's the show hoping to show you something to lead you to the right answer rather than telling you what it is (much like the mother/father middle ground). It might seem less abstract if it was more direct in the messaging and I suspect it won't get a third season which is a shame imo.