First of all with Ryan Air they want the Center of Gravity as far as possible to the rear border. This reduces the need to trim the aircraft and thus reduces the aerodynamic drag caused by the trim-elevator. This in turn saves fuel...
As with the Embraer as with all other aircraft there is a maximum take-off and landing mass that has to be complied with. There is also a minimum amount of fuel the aircraft has got to have for emergencies or extra holding in the air. I can only speculate that the captain of the Embrear was adhearing to these regulations regarding the amount of extra fuel the aircraft has to carry on-board...
As you can see this has nothing to do with the amount of runway there is available...
Kind Regards
Tim