Me no understand.
"Only the federal government could effectively resolve and enforce the resolution of conflicts between states."
Oh baloney. States take their conflicts to federal court and the commerce conflicts are resolved there. Congress doesn't even get involved. That was the original intent since that was the pressing problem at the time.
"And he is indeed talking about commerce among all the states."
Just read your own cite, for crying out loud. Madison illustrates his point by saying, "by the importing States in taxing the non-importing". That's not commerce among all the states. That's an example he's giving of some states (the importing) committing an injustice (taxing) on some other states (the non-importing).
That has nothing to do with Congress passing some general commerce regulation on all the states.
"Going by the original intent of the Commerce Clause, the substantial effects doctrine is a fraudulent exercise of power."
Going by the original intent of the Commerce Clause, the substantial effects doctrine is not even relevant. It's only relevant when it comes to Congressional regulation.
The substantial effects doctrine is not relevant to the original intent of the Commerce Clause because it is not and never was part of that intent.