Until last year, what Ryanair was doing was legal in Europe (even though the French law would beg to differ with this )
Since June last year their "non base" in Marseille has given the French the golden opportunity to nail them utilising a law that has now been adopted in Europe. The crux of the matter is whether French or European law will hold sway, as I am guessing the level of fines/back-payments dates back to pre Jun12.
Interesting linkie here
The airline base concept: European LCCs love to base aircraft and crew abroad, unlike others | CAPA - Centre for Aviation