Should an ERP system allow flexibility in procedure or not? and if so should it be similar for a large and medium size companies?

Oh yes every good ERP allows Flexibility and it is a basic requirement for the larg organisation that ERP allows them to easily cope their requirement. but this flexibilities does not means to totally change the ERP system rather the organisation must try to adopt the ERP in its actual sence to get the better results  

An ERP system meen Enterprice so is already targeted for Big companies! Flexibility is a must! And the important part is in the process optimization.

ERP solutions enables you to integrate all your organizational data into one comprehensive environment to streamline operations and improve decision-making with real-time data.

but keep in your mind that you have to customize your system to be matching with company size .