The tables that were imported from the original dataset use MyISAM as their storage engine. In MySQL 5.5 and later, the default is InnoDB. Since the Python scripts don't specify an engine when creating any new tables, these will use InnoDB while the tables from the original dataset use MyISAM.
The InnoDB engine provides foreign key referential integrity constraints, while MyISAM does not. If you try to define a foreign key when creating a new table (which will use InnoDB by default), you won't be able to relate it to a column in a table that uses MyISAM. For example, when creating a relationship between the table 'alert' (InnoDB) and 'patches' or 'files_*' (MyISAM).
For more information on MySQL storage engines, refer to this page.
How important is this issue? Should only one type of engine be used (use MyISAM for new tables, or convert any old ones to InnoDB)?