I am pretty sure I just do something fundementally wrong, guessing my way 
But it looks like that edting the database options per Target required a new start of Wappler. After I added all database settings (tried a couple of times now) and quit Wappler after each editing, they are stored now.
When I change the Target on the Publish Dialog, it seems to write the correct database settings into /app/modules/connections/...json
Is this actually the correct process to set it up?
Local Development settings:
Switching to another Target, no changes in settings dialog:
Quitting Wappler and re-opening, data as expected
After I did this now for both enviroments, the publish process creates the correct files.