but my point is that outside of that experience the other evidence doesn't stand up, the evidence supporting Mormon story is nowhere near strong enough to convince a non-believer
And right there you have hit on the exact point.
To circle back to the point of the article I think some people think the evidence around the stories is solid, and that's a big part of the reason they believe. The Internet exposes them to strong counterarguments, when they realize the stories don't stand on their own that damages their faith as a whole.
To be clear, I do think the evidence stands up to scrutiny, as long as you look at all the evidence. It's not that I'm afraid of academic debate. I would not be ashamed to build a hypothetical court case to try to an impartial jury (as if there is such a thing) in favor of my faith. I am confident that I could convince an impartial jury, by a preponderance of the evidence, that I am right. But as you point out, that evidence would fall far short of producing in my jury the kind of conviction that would lead them to commit their entire lives to a cause. When we speak of faith, we do not speak of blind belief. Faith is a vital force that leads to "being doers of the word, and not hearers only," and that fundamentally changes men and women internally. "Preponderance of the evidence" doesn't cut it. It's an interesting academic exercise, but ultimately worthless to producing any kind of meaningful, vital faith.
To the point of the original article, I have personally known several former Mormons who have left the Church of Jesus Christ of Latter-Day Saints over stuff they read on the internet. And I myself have learned many things as an adult that I did not know as a child, when my faith was still nascent. Confronted with those things, I had to ask myself honestly, "Do I still believe this?" The incontrovertible answer to me was (to return to our analogy), "Yes, this is definitely a tree. I have seen it and felt it. I have tasted its fruit. It is what it claims to be." In my opinion, that is also why so many leave when confronted with difficult questions. It's not that the evidence is so totally compelling, or that it can't be answered. It's that they have not had the deep, personal, individual experiences. They have relied on their parents' faith, or on momentum, or on social pressure, but they have never tasted the fruit personally, or if they did, they did not recognize it. Lacking that individual witness, they begin to feel they have been deceived, and that makes them angry. This is why we send missionaries out armed not with scholarly articles on the Egyptological basis of the Book of Abraham (for that you might try Hugh Nibley's An Approach to the Book of Abraham, but rather with blue paperback Books of Mormon. Their message is not, "Here are a bunch of evidentiary points that support the Book of Mormon," it is "Here is the book itself. It contains God's word. It was translated by Joseph Smith, who saw God the Father and Jesus Christ [not as part of a tree analogy, but with his physical eyes; a claim I do not make], and who was a prophet. If you want to know if the book is what it claims to be, read the book itself. It contains a promise you can test---that if you will personally read it, ponder on it, and then ask God if it is true, he will manifest the truth of it to you." This "manifestation" is the other sense I spoke of, one that we all have, and one that we have probably all experienced at some point, but that we must sensitize ourselves to.
Thus, to your point:
You don't believe the Books of Mormon and Abraham are factual because they stand on their own, you believe because they're endorsed by your faith which you believe for other reasons.
I would say quite the opposite. The books stand entirely on their own, because I have experienced the value of what's in them. I don't need an outside authority to tell me what to think about them. From that context, the story of where they came from and how they came to be is certainly interesting, but ultimately secondary. If I give you an apple and you eat it and find that it tastes good, the apple stands on its own. It tastes good regardless of where or how I got it. The apple is good even if you discover that the tree has some curious and unfortunate blemishes in the bark (we do not claim infallibility for our prophets or our members). The apple is good despite the latest cutting-edge research in biochemistry that has convinced many people who have never tasted an apple that they do not taste good. But you are correct that once I know the apple tastes good, that will color my perception. I will believe that the blemishes are only surface blemishes, because a tree that is not fundamentally sound cannot produce good fruit (i.e., Joseph Smith was not perfect, but neither was he an adulterer). If the latest research concludes that the apple can't taste good ("Cosmologists have discovered X about the CMBR, totally disproving God!!!"), I will not have a crisis of faith and think I must be wrong about the apple, because I have tasted it, and continue to taste it every day.