To give a real life example the company I used to work for had a fleet of B-757s. They were based all over the country with the furthest summer destination during the summer being Pafos.
All the aircraft had a similar structural MTOW that was certified by Boeing. However the aircraft based in Glasgow require more fuel to fly to Pafos than an aircraft based at East Mids (Its further away). Therefore the Glasgow based aircraft was certified by the CAA to have a greater take-off weight than the EMA aircraft although both are lower than the Boeing structural MTOW. i.e 103,999 kg rather then 98,999kg both less than 115,000kg structural weight.
If during the summer a Glasgow aircraft went long term tech and was replaced by an EMA aircraft the CAA would be advised and the certified weight changed. During the winter some aircraft were flown to the USA of Xmas trips. These aircraft were recertified up to the maximum structural weight due the extra fuel required.
These changes were not done on a sector by sector basis but on an 'as required' basis. As has already been stated Eurocontrol charge for use of the airways on a weight band basis i.e. its cheaper to be at the top of band C than the bottom of band D, like council tax.
What Ryan Air appear to be doing is claiming their aircraft are band C weights and then flying at band D weights therefore avoiding the extra charges. Tax evasion, fraud, incompetance, honest mistake, call it what you will.
I hope this helps.