And that sound you hear is me going "So?"
No one except Napoleon of the leaders of the Great Powers wants Napoleon dominating Europe the way "I'm going to rebuild the Carolingian Empire" would mean.
Not Austria, not Prussia, not Britain, not Spain, not Russia.
Also, Napoleon leaving Portugal out of the Continental System ruins the entire point of it as a policy.
You want to avoid war in regards to France and most everyone else, avoid "France wants to dominate Europe" war in the first place. Because no one is going to happily accept someone as conquest-happy as it would take to take those lands - and Britain will eagerly fund Austria and anyone and everyone else that will fight it.
Napoleon isn't the one trying to recreate Charlemagne, it's the reaction after 30 years of his tyranny that does. I don't know why Napoleon couldn't have just included Portugal as one of the nations who imports he banned after all he would've had a much easier job of stopping cross border traffic than sea borne smuggling.