According to the article, the gist of the debate between Lincoln (heir to the Federalist tradition) and the Jeffersonian anti-Federalist tradition is whether the US would be a commercial/manufacturing economic power or an agrarian nation. I agree that ultimately it's THIS question, rather than tariffs/free trade or slavery/anti-slavery was the fundamental divide between Federalist and Anti-Federalists, and the ideological difference between Union and Confederacy.
Except that an awful lot of farmers fought for the Union, and some aspiring industrialists supported the Confederacy.