The flaw I perceive in your OP is that you start out talking about one thing and then try to prove something else.
the use of the Bible and other 'historical' literature to generate knowledge about the physical world
You then go on to a story of a young man using the scientific method to find out what his tribe's origin stories are.
Those are two completely different things. The Bible is a perfectly permissible, scientific source for information about the origin stories and religious practices of ancient Jews and early Christians. It's frequently used this way by investigators of all religions. The Bible is a completely illegitimate source for geology, human history, biology, cosmology, and the like, and there is by definition absolutely nothing scientific at all about misusing it for this purpose.
Utlimately this is representative of the faulty thinking that science is about particular sources, when in actuality, science is about the method of manipulating and interpreting those sources.
Absolutely wrong. Science is both a means of deriving conclusions from sources
and a means of judging which sources produce reliable information about the physical world, and the context in which that information is probative. Science
is a source - it's a source of information about the reliability of sources. If your young man fails to apprehend that his parents are the Villiage Liars, or apprehends it but accepts their testimony at face value regardless, he's failing to appropriately apply the scientific method. Ultimately, the scientific method is one of skepticism about sources. Your position is one of complete credulity towards a particular, unreliable source. Nothing about that is scientific.