Let's play the hypothetical game.
I open a factory in Rhode Island. It burns fish guts all day long, and sells the ashes only to people within Rhode Island. But, the smoke blows across the border into Massachussetts, and fills your home with nice tasty fish-gut smoke. Maybe it gives you a delicious case of AIDS or something.
Massachussetts can't do a single thing about it, because the factory is in Rhode Island. Rhode Island won't do anything about it, because it's good money for Rhode Island.
Under what you're getting at, you're screwed. The Federal government would not be able to mandate the installation of something like a filter on the smoke stack, because there's no "interstate commerce," as you seem to be defining the word.
But, fortunately for you, that's not what the situation is. That factory affects interstate commerce, in one way or another, so the Feds tell the owners to either install a filter or pay to remediate your property and hold you harmless.
And that's how it works. That's why we have the interstate commerce clause, because before it existed, under the Articles of Confederation, the "United States" was mass pandemonium.
The reductio ad absurdum of "well, everything is interstate commerce" is simply...absurd. Not everything is interstate commerce; in fact, the incredibly overwhelming majority of things are not interstate commerce.