You're reading more into his statement than what he said. He said that it was not the purpose of the commerce clause, as regards interstate commerce, to give the federal government power to regulate for the positive purposes of the country. He didn't say that Congress could do it as long as it abided by certain conditions. He said that it was not part of the power granted to it.
I think Madison was concerned about the use of the word "regulate". If the word allowed Congress to tax imports for the positive purposes of the country, then read literally, Congress could tax/tariff the products of a state for the positive purposes of 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).
But you're basically correct that he was concerned about the understanding of the phrase "to regulate trade". In his first letter, he gave a very broad definition of the term, saying that it practically synonymous with the encouragement of manufactures. He then wrote his second letter as an afterthought, saying that such an overbroad definition of the phrase should not be applied with regard to Congress's power over interstate commerce. His use of the words "negative" and "remedial", in that context, clearly apply to the nullifying of state laws that commit injustices against other states. In effect, he's saying that the power "to regulate commerce among the several states" is the power to restrict the ability of the states to regulate commerce with each other.
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.