That is not the standard explanation. That's a sound-bite. Lee did not resign simply because he happened to have been born in the State of Virginia. Virginia happened to be the home of his family and friends, the final resting place of his ancestors, the culture that made him who was he was, the source of his beliefs and values. Lee wrote, "With all my devotion to the Union and the feeling of loyalty and duty of an American citizen, I have not been able to make up my mind to raise my hand against my relatives, my children, my home." That's a long way from resigning "simply" because he was a Virginian.
You correctly, in my opinion, accused the author of the article in question of speculating a revisionist view of history. But how is your line of speculation different? General Lee wrote candidly about his decision to resign his commission. Nothing credible has been uncovered in the last 147 years which casts any doubt on his honesty regarding his decision. Your speculation that Lee was made privy to the Federal government's war plans, or that there was some other dark and mysterious motive, is purely and simply an attempt to revise history. I don't know why your posts always seem to hint at conspiracies. Sometimes, things ARE as simple as they appear. I think you're drilling a dry hole here.