But it does not appear to have any effect.
What happens exactly (or what doesn’t)?
I have written and attached a little BaseX command scripts that simulates the GUI workflow. You can download it and run it with BaseX on command line (it will create a temporary sub directory in your folder):
basex simulate-gui-db-creation.bxs
It should return the following output (i.e., the contents of the .xml and .dita document that are created in the first section of the script; invalid.xml will be ignored when creating the database):
<dita/> <xml/>
Does that help?