Perhaps I encountered a bug or my configuration is faulty.
I cannot change the permalinks structure in the default Settings > Permalinks
views without introducing the /index.php/
-part. This behavior does not change, whether the user is a Super-Admin or a regular Site-Admin.
However, as a Super-Admin, you can overwrite the permalink structure in the network management view
Your websites > Websites > All websites > (YourSite.com submenu) Edit > Settings > permalink_structure
.
Using this, I was able to get rid of the pesky /index.php/
part.
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