Making A Non-Issue into A... Non-Issue

Relatively new commenter Shalmo has repeatedly try to point out that the claim that the Torah we read today is the same Torah Moshe Rabbeinu, a"h, received at Sinai, is specious. He even helpfully provided a link which I follow up on. He has repeatedly said that he is patient awaiting my reply to his challenge and until now, due to Shavous, I have been unable to respond. But it ain't Shavous no more, eh?
The first point is that he uses the Samaritan Torah as a reference. The reason for this sounds logical. While the masoretic text of the holy Writ underwent multiple editing jobs until fairly recently in history, the Samaritan Torah did not. Therefore, if the Samaritan Torah is based on ours, it potentially represents an older, unaltered version of our Torah and discrepancies can be used to prove that our manuscript was altered at some point.
To answer this challenge, I would like to note the parameters I am working with.
First, how do I define a significant change in the 'script? No one except those living in deepest, darkest Me'ah She'arim deny that the Torah we read from today has minor differences that have crept in over history. There are the famous tikunei Sofrim, there are the cases where an aleph and hey get alternated, etc. There is even a comment somewhere in Vayikra from Rashi where he complains about the superfluous presence of the word "et" while in the text the word itself does not appear. Therefore I will not take the position that our Torah is, letter for letter, the one handed to Moshe Rabeinu at Har Sinai.
So for me a significant change is one that is consequential. Consequential, in turn, means that there is a halachic significant to the change. For example, if there is a variant fragment out there that says that Noah's sons were Shem, Cham and Archie, for example, who cares? It does not change the halacha. From this perspective, it is important to note that no such important changes exist.
Further, using the Samaritan text is also problematic. There are multiple versions, including one that is considered authoritative but without huge amounts of evidence to support the claim. There are a couple of major changes that they have made to the text (switching mountains in one instance to fit their own personal history). Further, according to our Bible the Samaritans maintained a level of idol worship even after accepting our Torah. I cannot see the logic of using another nationality's version of the Torah, one which is openly corrupted from the original, as a prooftext for ours.
The second point is to note that how one reads the Torah affects whether one sees certain incongruities within the text as problematic or revealing. For the academic who is looking for textual consistency in terms of narrative, grammar, etc., the Torah contains a whole host of problems. Narratives are inconsistent (compare the story of how Eliezer meets Rivkah Imeinu to the version Eliezer relates to her familiy), or repetitive (the two stories of the Creation of Man), grammar can sometimes seem to switch eras and spelling is erratic. This strongly points to the idea of either multiple authors or excessive editing over the centuries.
However, a believing Jew who approaches the text armed with the right commentators including the Gemara quickly learns that every single possible problematic part of the Torah is actually revelatory. Supposed mistakes or inconsistencies are meant to teach lessons, or shed light on applications of the Oral Law. Two specific commentaries which resolve most of the problems academics raise are those of Rav Shimshon Rafael Hirsch, zt"l, and the Netziv, zt"l, who both toil to show that the entire Oral Law is references through the Written Law and that there are no superfluities or mistakes in the entire text.
For those on the outside, this is seen as an exercise in apologetics but again, that's because they insist on, a priori, approaching the Torah as a piece of literature. If one refuses to see it as the word of God, then all the implications revealed by religious study of the text become irrelevant.
My final argument in support of this is what I call the "Ezra wasn't an idiot" argument. Many documentary hypothesis supports suggest that the Torah we have today is actually a synthesis of multiple (four or five) previous religious documents, each of which held authority in a different part of the Jewish people. For example, the Kohanim lived according to what we call Vayikra. Ezra, in an attempt to rebuild the Jewish people, took these documents and "redacted" them into a single document to create a false but necessary common history including a shared revelation at Sinai.
Never mind that no trace of these four or five separate Torahs has ever been discovered. While lack of his restaurant receipts is enough for academics to "prove" that David HaMelech, a"h, never existed, lack of existence of proto-Torah scrolls isn't proof of absence to them.
But what really strikes me about the idiocy of the DH hypothesis is that it assumes Ezra was a lousy editor. He left in spelling mistakes, didn't make grammer consistent, left inaccuracies between adjacent verses and so on.
Now, speaking as a (secondy) character in a fantasy fiction trilogy, I know something of how books are edited. The books I feature (somewhat) prominently in underwent multiple drafts and edits to ensure that spelling mistakes and inconsistencies were removed from the plot. And while they are breathtaking works of fantasy fiction they do not have quite the historical importance of a book like the Torah. Now imagine you're Ezra and you're trying to convince people that the scroll you're handing out to them is a God-given document. Are you really going to allow spelling mistakes for people to point out? Please.
In conclusion, when one reads the Torah as a religious work instead of an academic one, there are no problems with finding oddities in the text.