Why mention God? If you're attempting a scientific stance, starting your initial question with an unproven deity who doesn't want us to eat meat on Fridays part of the year, why? Why include that, it's an instant turnoff to any evidence-based reader.
I'm an atheist myself and find no issue in the use of the word God here. We don't know with any certainty how the universe was spawned into being, using God as a sort of shorthand to state as much isn't a problem.
I don't think there is a problem in mentioning God as a shorthand for "whatever caused the universe to be the way it is and cannot be proven". Like axioms in maths, you need some unproven assumptions to do something, otherwise you get ridiculous situations like Boltzmann brains.
Q1 could be understood as "why is the universe so weird as to require quantum mechanics?" It is undecidable, just like god is, but it makes the point that quantum mechanics may take us a bit too far. For example, it may result in said Boltzmann brains, and once you get to that point, the science become meaningless.
The maths of quantum mechanics check out, this is unquestionable, but the article is about the deeper implications, at the limit of philosophy. If you are in the "shut up and calculate" camp (which is fine), it may be meaningless to you, but I don't think it is an unscientific debate.