I can see how you would be confused. The difference is that Nismo is and has always been a part of Nissan, but they used to make super low number special cars completely separate to the Nissan production facilities. I believe they still do this as they have recently had a lot of investment and a new premises. However alongside this Nissan has now started to release Nismo performance versions of their original road cars. These cars aren't built by nismo but by Nissan, so belong in the Nissan dealership.
Interesting fact, the new GT-R Nismo was actually developed by Williams so actually had little to no input by Nismo themselves. In other words, theyre just trading on the name.