FR will not have exceeded the aircrafts MCTOM period.
What they may have done is declared one flex MTOM and operated at a higher weight, its not a safety issue as such, but if this is any more than an omission by the flight crew on a particular flight and is as widespread as the report suggests then repercussions may well be serious.
For those who don't quite understand this system let suppose an aircraft is doing a 4 sector day sector 1&2 DUB-STN-DUB mainly hand luggage TOM say 61000kgs sector 3 & 4 DUB-AGP-DUB full flight and lot of hold luggage TOM say 74000kgs so on the first two you pay Euro fee's based on 65T and on 3 & 4 you pay fee's based on 75T
What is alleged here is that Ryanair have deliberately declared a lower TOM when the actual was higher for no reason other than to lower their costs, where that to be proved (it wont be difficult to prove/disprove) then legal action will almost certainly follow, if this was proved to be deliberate and systematic across Europe heads will roll and the directors may face legal action themselves, suspension of their AOC could follow.
All airlines will likely face more SAFA checks now so make sure you have your doc's in order and your spare glasses!!
Airlines with EFB's normally require the commander to sign (electronically) that they have declared the correct TOM and with some airline change the ATOM plate in the flight deck for each flight at a different TOM i.e. 65T or 75T
Its hard work being an Ultra Low cost airline, but the list of questionable if legal practices continues to grow for FR what goes around comes around