There is such a check, but it only applies within the "same import". Imports are currently considered different based on the database they are coming from. While source = off, the source database is the target database (like if you had uploaded your MW tables via phpmyadmin into the same database with your XF tables). If you ended up with duplicates, you should use Wiki Admin Panel > Maintenance > URL Conflicts to identify and manage the duplicates.
The phrase issue should be fixed in the next version.