That's the reason they're charging £/€8 for the check-in option to encourage priority boarding and avoid just shifting the problem to check-in. Getting the right number of people and bags to turn up at the gate is the optimum solution to the problem.
Wizz now have a nearly identical system however they don't charge to check-in a cabin bag. Sounds great on the face of it but think how many people must opt for the free check-in option and the overhead lockers end up flying half empty as only say 30 pax forked out for the priority option. I cant comment from personal experience but it must make Wizz check-in a nightmare, or cost them an awful lot in extra resource.