Under the hood, the Super Table fix is running a migration behind a controller, which you can call in a content migration directly in your project. I have done the same, due needing to script it in a deployment.
<?php
namespace craft\contentmigrations;
use craft\db\Migration;
use verbb\supertable\migrations\m190120_000000_fix_supertablecontent_tables;
/**
- m190412_102156_fix_super_table_content_tables migration.
- Runs the fix content table migration part of Super Table plugin
*/
class m190412_102156_fix_super_table_content_tables extends Migration
{
public function safeUp()
{
echo " > Starting migration for fixing Super Table content...\n";
(new m190120_000000_fix_supertablecontent_tables())->safeUp();
return true;
}
/**
* @inheritdoc
*/
public function safeDown()
{
echo "m190412_102156_fix_super_table_content_tables cannot be reverted.\n";
return false;
}
}