The German findings in future about fare structures etc will still transaction and by transaction have to be EU regulation compliant. The arguments you put forward could only be evaluated once they have past the clarity test at the point of booking. If the airline didn't give a precise warning when booking all the following arguments are moot. I think that the thread keeps overlooking the clarity issue.
On EU compliance, the relevant German legislation and caselaw uses the same test of good faith that you find in the UTCC Directive.
I would agree with you that there is a potential issue with clarity and it is the more promising argument but it is anything but black and white. Clearly, you cannot highlight every single clause in a contract in the booking process. On balance, I would agree that there is probably a reasonable case based on the UCCTRs (or corresponding provisions implementing the UTCC Directive in other EU Member States) but it is imo not an open-and-shut-book case