You have your current unwanted result with Lead #1 being in your list because it has a "duplicate" email address and is also False, so it shows up even though the its "partner" duplicant doesn't. Since the records aren't tied together you can't eliminate the "single" duplicate leads in your list without having some other type of field criteria that would keep them out of your list.
Filters work in order they are positioned and also apply the logic rules. So if your logic rule is set to
ALL filters and your first filter is
SFDC is Deleted = False then only those records that are false will pass to the next filter of
Duplicate Fields - Field Name is Email Address. (your current situation)
To filter out the singles you would have to add another field filter and possibly change the logic rule.