I happen to know a thing or two about Scientology. I also went and read a good deal of reviews from a website which is run by former high ranking members of the "Church". We are in agreement that this movie is more or less directly based on the life of L. Ron Hubbard. The references are made in many sequences of the movie, and many of Scientology's theories and verbiage are referenced throughout the dialogue.
However it is not an expose of the quasi-religion, or the imagined creation of another. They simply use it as a backdrop. It is more the story of one broken man who wanders into it. This movie is absolutely stolen by the performance of Joaquin Phoenix. Most people who see this film will walk away thinking about his character Freddie Quell, and even I had a hard time paying attention to anything other than his every unpredictable moment in this film.
I won’t spoil this movie for those who have not seen it, but it did make me think of the constant mentioning of Manson's connection to Scientology and the fact that Bruce Davis also has been connected to the church, and murder of two people who lived on a Scientology property. Just because helpless young people were slaughtered in such a brutal manner - do they have to drag up the usual suspects? If ever there were a group of people as dangerous and mysterious as the Manson Family- would not the Scientologists be among them? The Process, Scientology, Church of Satan? Why do so many want to connect them to Manson? It seems there were no shortage of fringe groups to join if you were a lost confused soul during this period of time. Why do you suppose that some chose the darker ones during a time of so much promise, hope, and light???