Because there is more to a political ideology than whether it is libertarian or authoritarian. For example, you can have two authoritarian governments, one of which requires everyone to be an atheist (Communism), another that requires everyone to belong to a state-sponsored religion (Islamism). Even though both are authoritarian or totalitarian, obviously, an atheist dictatorship isn't going to get along with a religious fundamentalist dictatorship in the long run.
Along the same lines, in spite of the fact that Stalin's USSR and Hitler's Germany used many of the same methods, their goals were opposite. National Socialism was nationalistic and rooted in social Darwinism, Communism (at least in theory) was anti-nationalistic and egalitarian. Communism was driven by class warfare - all private property was confiscated or abolished in the USSR. The Nazis, at least in theory, allowed powerful industrialists, bankers, and the aristocracy to maintain their property and wealth, and in fact saw differences in wealth and property as part of the natural order that they wanted to maintain.
So as far as the Nazis and Communists were concerned, the fact that they both had totalitarian systems of government was incidental, what mattered was that they tried to implement opposite worldviews with totalitarianism.
Great feedback, thank you for taking the time to respond so thoroughly. I appreciate it and even though I had realized the different approaches, I had not really compared their ideology to those levels. With your prompting, I have a better understanding and approach to my thinking about the subject.
You are right, evil is not something to be generalized into one single box. It has many faces and sometimes those faces are in direct competition for our destruction.