It's not that confusing.
Imagine for a moment that the European Union becomes a unified federal country (and it's actually not that implausible as mid-term scenarios go...), with one president ruling over the 27 countries.
Spain would then cease to be a country in its own right, wouldn't it? But it would still retain its culture and history -- its civilization, if you will. In other words, there would still be a distinct Spanish culture, different from the French culture and the Italian culture, even though they all would be simple regions ruled by Germany one elected president.
On the other hand, would you say the mix of cultures and peoples that that "United States of Europe" would comprehend are part of the same civilization? (you can argue that they're all part of the Western civilization, but then you're entering another level of comparison).
What Felis is saying (as I interpret it) is that England is a different civilization -- as in, represents a different culture, people, and history -- than Scotland. The United Kingdom is a nation-state that unifies those different civilizations under the same rule.