Your entire argument boils down to "the USA won". Goes back to the one who wins writes the history.
Yes and no. The nuance here is that we are talking about Lee's US citizenship. Everyone agrees he was a US citizen in early 1861, so how and when did he lose it is important as that will be the crux of the original question Pb and I were discussing: Did Gen Lee commit treason against the US.
There are generally two ways you can get rid of citizenship. You can renounce it formally, or it can be stripped by the country. Case in point: I was born in Italy and had dual citizenship until I was an adult. I needed to formally renounce Italian citizenship to get my security clearance. Simply joining the US Army didn't do it.
But back to Lee: There's no evidence he ever renounced his US citizenship. Indeed it would have been out of character for him as he considered himself a Virginian first than an American. We know the US government didn't do anything formal until after Appomattox because there are records of that. So after his resignation from the US Army, when he took up arms as commander of the Provisional Army of Virginia in Spring of 1861, how could he be anything other than a US citizen committing treason against the US Government. Hell the the Provisional Army wasn't even folded into the Confederate Army for a couple months after that.
Also, I repeat, Lee himself said several times that secession was nothing but rebellion. And if you are under arms in a rebellion, you are kinda by definition committing treason on the government you are rebelling against.
That's the No part. As to the Yes part, I feel like "the US won" is a pretty compelling argument since
what the US won was the question of; "Can US states form their own country and leave?" The answer is "No, they can not." Since the US won, and secession is unconstitional, those states were not a country, but rather states in rebellion against the government. None of this was even controversial until the 1930's or so when a CSA public relations push was made.
Gen Lee is simultaneously a gifted US Army Officer, a successful Superintendent of West Point, a traitor to the United States, the cause of tens of thousands of US Army casualties, a slave owner, and by all accounts an honorable man. Thus the confusion on his legacy.