Well of course going towards integration vs segregation is an organizational (in this case, political) decision. I was saying that the average EU state machinery has a lot of room for integration, should there be a political intention to go that way.
Case in point: in Italy, different towns used to have different systems for their resident registrations. I doubt there was an extreme need for customization in this context, it was just that bigger/wealthier towns had a chance to digitize earlier and so on, leading to extreme fragmentation. Moving to a nationwide register took literally a dozen years or so, for a single service of a single country.