If this tool is taking data directly from MySQL, why does it need to rely on column names to determine relationships? Couldn't it just see that a column is a foreign key?
See "Foreign key support" in MyISAM
Also, in my experience a lot of people do not always use the underlying database constraints even in InnoDB.
Not sure if that was the intent of the authors, but just so that others may understand that it could be more than just "PHP land". Might be a little closer to "MySQL land".
Being as they can certainly make for very rude surprises, when you discover them by chance.