Hi there,
I ran into the same issue with my page, and had hoped to find some solutions in here, as the initial post described my findings pretty well!
I have managed to find a reproducable error… in a video by Matomo, that was created around the same time as this discussion 
In here, he demonstrates how Matomo tracks the source of different kinds of traffic. When coming from an email (starting at 1:55), the traffic is listed as Direct again, which does not seem to be what he had expected.
Might be close to what @Lukas has described in terms of the referrer policy?
What I don’t get however is that Google Analytics does not seem to have this issue.
Additionally, what would be the ideal way to handle this?
Just add mtm-parameters to EVERYTHING that links to the page? This might disrupt the actual intended tracking of Matomo, as everything would then be considered to be campaign, traffic, and not be shown in “Social Media” or “Websites” anymore, right?