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I recently set up ghost on a regular VPS and it sends "internal" emails like 2fa and invites directly from the docker container as far as I can tell.
The sender is the server domain (and ip). (Which btw. gets flagged as spam in my case because I use that domain with tutanota...)
Only bulk/userfacing emails go through mailgun, as far as I can tell, but havent tested this yet in detail.
Maybe that helps you in debugging.
Thank you for your help!
We have fixed it - the problem was that I had already set up DNS records so that Tuta could send emails using our website domain. This was blocking the proper set up of mailgun/transactional emails.
So we worked out how to set up emails for the business separately using the SMPT email server of our web hosting provider - et voila! Email set up works!