Will MageMail affect transactional email that Magento sends?

No, MageMail doesn't touch any of the email functionality within Magento out of the box. However you can enable a welcome email, order confirmation email, or newsletter subscription confirmation email if you would like to.

However, if you have 3rd party extensions that are currently sending out emails that MageMail does send out, such as abandoned cart emails or review requests, you will want to disable those emails before enabling MageMail emails.