Subscribe2 simply makes use of the wp_mail() function in WordPress. This in turn uses the PHPMailer class that is included with WordPress and this then (in default configuration) uses the PHP mail function which uses the server 'sendmail' binary command.
So, Subscribe2 / WordPress emails are sent via PHP and not via any email server UNLESS there is a specific configuration employed that pushes emails that way. There are SMTP plugins for WordPress that over ride the wp_mail() function and configure it in a way to send your emails via an SMTP email server based on details you input iron the settings.
I also posted code a few years ago that re-configures PHPMailer to use an SMTP server without over riding the core wp_mail() function.
Okay, so once that done all emails in Subscribe2 or WordPress will be sent the same way. Perhaps the only difference will be the sender details. WordPress will set the sender as WordPress with a made up email address of WordPress@your-domain.com whereas Subscribe2 is set to use one of your administrator user accounts.