I have additional info.
This issue (additional body tags appearing where they shouldn’t be) appears to be related to signatures or images in mails.
I did some test without an attached signature, and suddenly we sent out emails with proper settings again.
I then took our default signature, which contains images, and removed said images.
It still worked fine.
After placing the images back into the signature, we instantly got mails with broken settings again. (Speaking about extra body-tags.)