No. In this letter, he said it was not the original intent of the commerce clause to give the federal government power to regulate foreign trade for the positive purposes of the country. The original intent was to prevent or correct injustice among the States themselves.
But he does not retract the statement in his earlier letter that it was fine to regulate foreign imports under the commerce clause for the positive purposes of the country. And from that, I say that it is also fine for Congress to regulate commerce among the several states for the positive purposes of the country (or against the negative purposes to the country).
"As I pointed out, there would have been little reason for him to be concerned about that specifically, since the Constitution already explicitly prohibited that (no taxes on exports from any state)."
Fine. Then change my scenario to Madison fearing that Congress would one day use its regulatory powers to ban cotton from Georgia for the positive purposes of the country.
It's at this point that I should recall the statement you made that prompted my initial response to you herein: "Do you believe the Founding Fathers would give Congress the power to regulate interstate commerce, yet allow the individual states to undermine and subvert their regulatory efforts?" Since it wasn't their intent to give the federal government power to place actual restrictions on commerce subsisting between states, it would follow that it also wasn't their intent to give the federal government power to restrict that which would allegedly undermine an attempt to restrict commerce subsisting between the states.
The actual exercise of a power may or may not have to conform to the original intent - that's debatable at least. But measures which are "necessary and proper" for carrying into effect a particular power would, among other things, have to be consistent with the reason for which the power was granted.
And from that, I say that it is also fine for Congress to regulate commerce among the several states for the positive purposes of the country (or against the negative purposes to the country).
So if I understand you correctly, you're saying that although it wasn't part of the original intent for Congress to regulate commerce among the several states for the positive purposes of the country, Congress nevertheless has that power. In that case, there was little point to Madison's second letter, beyond raising a matter of mere historical curiosity. I think Madison's reason for bringing it up was more than purely academic. That's the impression I get, anyway.
"As I pointed out, there would have been little reason for him to be concerned about that specifically, since the Constitution already explicitly prohibited that (no taxes on exports from any state)."
Fine. Then change my scenario to Madison fearing that Congress would one day use its regulatory powers to ban cotton from Georgia for the positive purposes of the country.
But there's still nothing in the letter that shows his concerns to be that Congress might unjustly discriminate against one state. Of course it would be unconstitutional if it did, but nothing indicates that that's the limit of his concern. He said that it wasn't the original intent for Congress to be regulating interstate commerce for the positive purposes of the federal government. Now either that statement reflects on the actual legal meaning of the commerce clause, or it doesn't. If it doesn't, then it can safely be dismissed altogether as mere historical reminiscing. If it does, then it means that Congress does not have the power to regulate interstate commerce for the positive purposes of the federal government. It's one or the other.