I'll have a go at this - bear in mind, though, that I don't participate in any of the Religion SEs, so if you disagree, do chip in.
Question 1: On-topic. It's a question about a story of the Christian mythology/religion, and can be researched and answered in a way consistent with questions from other mythologies. (For example, I'd put this on a par with Who was Theseus' father?, which has no close votes.)
This is also (I imagine) on topic at Christianity.SE. I don't see a problem with this.
Question 2: Definitely on-topic. It's a comparison between two myths and asking about potential links between them. I think this is fine, and even encouraged. I would be surprised if this is on topic at Christianity.SE.
Question 3: Tentative off-topic. There is an argument that it should be on-topic in the same way as Question 1 is. However, in the case of Question 3, it seems exceedingly specific to a particular phrasing of a particular text of a particular religion. Asking who a pronoun is referring to does not (or at least, does not seem to me) to require any expertise in mythology and the stories behind it - it seems like it would be best addressed to an expert biblical scholar. Given this, I suspect it is on topic at Christianity.SE.
Interestingly, though, the question does add "Were there any other people on Earth?" If framed as trying to figure out the correct story and mythos behind it, I think it could be on-topic. However, I do appreciate it's a fine line, so feel free to chip in with further opinions.