The issue seems to be ( if I understood the article correctly) between FR which declared all its aircraft to have a MTOW of 66,9 Tons , and the manufacturer data which says MTOW 75 Tons.
Actually, the issue seems to be a discrepancy between the MTOW declared by Ryanair and what is actually entered for the same airframe into the Irish registry. As the German DFS does not have direct access to the Irish registry they actually had to perform some ramp checks to collect the data and see if there was any discrepancy.
Actual take-off weight is of course irrelevant as far as ATC fees are concerned. According to the article actual MTOW was never exceeded.