Hi wolfl ,
Thanks for your post.
Unfortunately, there isn't an option in Settings where you can disable the automatic synchronization of the WooCommerce stock field and only allow calculating it when a cron is executed (please note that this is what you are doing with the calculated properties when enabling the CRON in settings).
If the synchronization isn't working in your case, you'd need to find out why. That shouldn't happen.
Anyway, you can execute the tool from the WP CLI interface. That allows you to create a cron to execute the tool:
wp atum pl_update_real_stock
I hope this helps.
Best Regards,
José Andrés