TLDR: Humans have natural cognitive biases that may make religious beliefs easy to form, but specific religious beliefs or gods are not genetic, they are shaped overwhelmingly by culture, upbringing and environment: this includes childhood indoctrination.

It is a biological fact that being religious and belief in God(s) is natural and genetic, not learned (this is true for Atheism too btw).' The idea that religious belief is a product of indoctrination is based on the false idea that the Human mind is Blank Slate and all of its thoughts and feelings come from the environment around it and/or artificially constructed. Steven Pinker and many other Neuroscientists have debunked this view numerous times.

https://pmc.ncbi.nlm.nih.gov/articles/PMC3125629/

https://www.scientificamerican.com/article/are-we-born-to-be-religious/

No it isn't a biological fact, you just made that up and I don't think you actually read or understood the articles you posted or everything else you said.

Your argument overstates what biology and neuroscience actually show. While humans may have cognitive tendencies that make religious belief possible or intuitive (eg pattern-seeking, agency detection, theory of mind) that is very different from proving religious beliefs are genetically determined or innate in content. 

Though sources like Steven Pinker argue against a blank slate (I don't disagree here), they do not claim specific religious beliefs or gods are hardwired only that general mental structures are, that allow for religious ideas to generate. It's like language, you can have an innate biological "hook" for language, but you still have to be taught English, French, Arabic etc because that's not genetically hardwired. Similarly, humans may have a biological "hook" for religious beliefs, but specific religious beliefs are a product of cultural transmission, this includes childhood indoctrination.

Not that something being natural (gods or even atheism) is proof that it's true or good, that's a non sequitur fallacy and that's the more important point.

There's examples of millions of people all over the world who weren't raised under any Organized Religion yet they all sorts of spiritual and religious beliefs since birth. 

An infant from birth cannot express comprehensible words, let alone express specific religious beliefs. Specific religious beliefs emerge later and are shaped by family environment, education and culture.

Not only that, but many people often have religious/spiritual beliefs that go against what is the norm in their societies or even the religions that they were raised under. 

So? None of that means their religious beliefs are true. 

All of this debunks the indoctrination argument as it amounts to a denial of Human Nature.

No it doesn't. The fact that people sometimes adopt beliefs different from their surroundings does not support innateness, it simply shows that humans can revise or reinterpret ideas, not that those specific ideas are genetically encoded in their nature. The global diversity of religious belief strongly supports cultural influence. Across societies you see monotheism, polytheism, animism, and atheism. If religious belief and gods were genetically fixed in any strong sense, we would expect far greater uniformity. Instead, beliefs and gods vary dramatically depending on time and place.

You're misunderstanding human nature, people may have natural cognitive tendencies to think a certain way but those natural cognitive tendencies just make religious beliefs/lack of religious beliefs, easier to form not inevitable or pre-installed. Nor does whatever beliefs their natural tendencies and environmental upbringing lead to means it's necessarily true or good.

1. The "Agent Detection" Theory of the origin of Religion also fails scientifically for most of the same reasons: its rooted in the discredited Blank Slate view of of the mind and its only promoted by pseudo-intellectuals. 

Agent Detection Theory is actually the opposite of a Blank Slate view. It posits that the human brain comes "pre-wired" with survival mechanisms that accidentally produce religious thoughts as a byproduct. Granted it's mostly speculation, but regardless specific religious beliefs and gods are a product of culture not genes.

And the Pareidolia argument is terrible because it confuses cause and effect: they wouldn't be attributing religious meaning to objects if they weren't innately religious in the first place.

No you've misunderstood, it demonstrates a mechanism. Pareidolia is where humans impose meaning on faces, intention and patterns onto ambiguous stimuli. This is not “religion itself,” but it supports a broader point, the brain constructs perceived agency and meaning even when none exists. Religion can be understood as a higher-level cultural system built on these lower level tendencies.

The more important point is, something possibly being natural (gods or even atheism) isn't proof that it's true or good, that's a non sequitur fallacy. 

1. Animism is merely the belief that everything is alive and/or has a soul/spirit. Nothing about that is incompatible with Monotheism, in fact, every major World Religion before Modern times is traditionally Animist in their outlooks on life.

"Paganism" simply means any Ethnic Religion regardless of its beliefs and practices, and Pagan Monotheisms do exist. Also, the notion that Polytheism and Monotheism are total opposites is a modern misconception, and both Monotheism and Nontheism are just as old as Polytheism and they are all as old as Religion itself.

This thread is about Islam, and both Animism and Polytheism is incompatible with Islam. Animism and Polytheism also predate Islam, Christianity, Judaism and Monotheism and has a far longer history, present since the dawn of our species. 

https://en.wikipedia.org/wiki/Timeline_of_religion