It uses this code:

						$primary_key_stmts = $this->sql_create_primary_key($table_name, $table_data['PRIMARY_KEY']);

						foreach ($primary_key_stmts as $pk_stmt)

						{

							$statements[] = $pk_stmt;

						}

Problem is sql_create_primary_key returns this:
return $this->_sql_run_sql($statements);

When return_statements is false (defaults to false) it then runs the query (trying to create the primary key for a non-existent table and returns bool true) instead of returning it.

Later on in the function it is done right where it handles the keys, it sets the return_statements to true.