Hi,
Thank you for your question regarding the mail settings in Acymailing and Joomla's global config. I can confirm that they are not related in any way. For Acymailing, you need to configure the send settings in the Acymailing interface, and Acymailing will ignore the settings configured in Joomla global config.
Joomla global config is for sending system emails, and when Joomla sends these emails, it will use the settings configured in the global config. If you would like to send your system emails using Acymailing, you can use email overrides as documented here: https://docs.acymailing.com/main-pages/email-overrides