Did more research after I got home, this time on German web sites including government ones. As expected found nothing to support the screener's view that unmarked bottles are not allowed.

To make absolutely sure I then contacted the German Ministry for the Interior (using their webform) - just had a reply confirming unmarked bottles are NOT prohibited.

Found out something very interesting in the course of my research: The EU version of the liquid ban is laid down in EU regulation 1546/2006. I tried to find the full wording of that regulation and it's nowhere to be found. Reason: It's deemed to be secret!

No wonder there is so much uncertainty and confusion if the full rules aren't published anywhere!