This is a pretty thorny issue. Theoretically, Marketo would reject such dupes or warn you when new ones occur with that email if they attempt to enter another LP. I forget the exact rules on this.
But you are right that you can't just figure it out. Because your smart list could say.
Dupes: Email Address
Lead Partition=1 OR 2
and you wouldn't really know where the dupes are unless your Lead View shows Lead Partition, which it can do. Then you can download the list.
BUT, you may not see dupes by Name, etc.
so I'd recommend processing dupes in another system and perhaps flagging them by SFDC ID to better identify these cross-partition issues.
I believe there's another way using Field stamping or something.