@nilss Thanks for the comment.
That is correct. The Mudita Phone app handles notifications through a closed channel that is not available to 3rd party apps. The mudita phone sends an empty notification in the system, doesn’t say Incoming/Missed or anything like that publicly.
So the only solution was to have a fallback for empty notifications that’s why you see “Notification received”. Couldn’t think of a better phrase to use because there might be other apps that send empty notifications 
You don’t see Mudita Phone notification in home notifications because those are cleared automatically from the system. In the “Letters” page all notifications are cached so that’s why you get the “Notification received” even though the Mudita system has deleted it automatically after the phone stopped ringing.
It works normally in other Android phones because they use proper standard notifications for the Phone app. This was all I could do and I spent a lot of hours on this problem but sadly it is out of my control.