I started working on a comparison between "The Master" and Scientology. Here's what I got so far...

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Film: Lancaster Dodd is the leader of “The Cause”.
Reality: Lafayette Hubbard was the leader of “Scientology”.

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Film: Dodd sails on a ship named Alethia. Alethia is Greek for “the state of not being hidden, the state of being evident”.
Reality: Hubbard sailed a trio of ships, the Apollo, the Athena and the Diana. Apollo was one of the most important and complex of the Greek gods. Athena was a goddess of wisdom, courage, inspiration, etc. Diana was the goddess of the hunt, the moon and birthing. Also, Diana Hubbard was his oldest child with Mary Sue and sailed with them as their “Lieutenant Commander”. (Fun fact. The ships were originally called the Royal Scotsman, the Avon River and the Enchanter.)

References: "Bare-Faced Messiah"; "A Piece of Blue Sky"; "Inside Scientology"

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Film: Dodd tells Freddie he’s “aberrated” and that he’s “wandered from the proper path.”
Reality: “Aberrated” is a common Scientology term, meaning “a departure from rational thought or behavior… The word is also used in its scientific sense… departure from a straight line.”

Reference: Scientology glossary

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Film: Dodd believes he knew Freddie in a past life. There are numerous references to past lives throughout the movie.
Reality: Past life memory is a key factor in Scientology’s doctrines.

Reference: Scientology FAQ

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Film: Dodd says he is “a writer, a doctor, a nuclear physicist, a theoretical philosopher, but above all I am a man...”
Reality: Hubbard was a prolific pulp fiction writer for years before starting Dianetics. He gave himself a “Doctorate of Scientology” degree, from the Sequoia University. In the book “All About Radiation” Hubbard calls himself a nuclear physicist, despite the fact that he never finished his studies. This has been retconned in his official biography to state that he attended the first class in nuclear physics at George Washington University but dropped out to explore life. Also Hubbard has written that he is a man, just like anybody else. As well there are a series of booklets devoted to Hubbard’s life, called “The Ron Series”. “Ron the Philosopher,” “Ron the Explorer,” “Ron the Writer,” etc.

References: "All About Radiation"; "The Ron Series"; "The Truth About L. Ron Hubbard"

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Film: Dodd performs a wedding ceremony.
Reality: Hubbard performed numerous Scientology wedding ceremonies in his days.

References: Scientology wedding ceremony

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Film: Dodd’s wife, Peggy, was originally named “Mary Sue” in the screenplay.
Reality: Mary Sue Hubbard was married to LRH for 34 years.

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Film: Dodd has two children from previous marriage(s); a son, Val, and a daughter, Elizabeth.
Reality: Hubbard had three children before he wed Mary Sue. L. Ron Hubbard Jr. and Katherine May Hubbard with Margaret Grubb. Alexis Hubbard with Sara Northrup.

References: "Bare-Faced Messiah"; "A Piece of Blue Sky"

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Film: Dodd gives a wedding toast and references a “cycle, like life. Birth, excitement, growth, decay, death.”
Reality: In Scientology, the basic cycle of life is “Create, survive, destroy.”

Reference: "Scientology: The Fundamentals of Thought"

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Film: During his wedding toast, Dodd deviates into an analogy involving taming a dragon.
Reality: Often in his recorded lectures, Hubbard would give humorous analogies involving fantasy and sci-fi elements.

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Film: Peggy talks about Dodd spending too much time defending himself from attacks.
Reality: Hubbard had made many references to attacks against Scientology by the AMA, APA, FBI, IRS, etc.

Reference: Wikipedia

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Film: Peggy emphasizes “ex-wives” when listing Dodd’s attackers.
Reality: In a 1967 interview, Hubbard denied having a “second wife,” referring to Sara Northrup. Hubbard wed Sara while he was still married to Margaret Grubb. Both marriages ended in divorce. Hubbard and Northrup had a daughter, whom he later disowned.

References: Interview "The Shrinking World of L. Ron Hubbard"; "Bare-Faced Messiah"; "A Piece of Blue Sky"

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Film: Dodd is writing “Book Two”.
Reality: “Dianetics: The Modern Science of Mental Health” is commonly referred to as “Book One”. But his second book, “Science of Survival,” is never called “Book Two”.

Reference: "Dianetics: The Modern Science of Mental Health"

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Film: The Cause’s form of counseling is referred to as “Time Hole work.”
Reality: Scientology counseling revolves around locating painful memories on your “Time Track” or “Whole Track”. (Formula: Time + Whole - W)

References: Scientology website; Scientology glossary

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Film: “Time Hole work” is done with the patient reclined and eyes closed, with the counselor sitting upright. The counselor guides the patient through the incident as if it were happening currently. (“How are you feeling? What do you hear?”) The patient speaks in present tense, “She’s saying…”
Reality: Early Dianetics counseling had the patient (“preclear”) either sitting or reclining with their eyes closed and the counselor (“auditor”) sitting upright. The auditor guides the preclear through the incident as if it were happening currently. (“What do you hear? See? Etc.”) The preclear speaks in present tense, “She’s saying…”

Reference: "Dianetics: The Modern Science of Mental Health"; "How to Use Dianetics"

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Film: A chalkboard shows a circular diagram, with phrases “This life,” “Pre-birth,” “Cellular level,” “Conception” and “Previous life.”
Reality: Dianetics (Book One) goes in detail about finding pre-birth incidents and casually mentions “cellular level” and “past life” incidents. A later book (“Scientology: A History of Man”) goes in depth on these latter concepts.

Reference: "Dianetics: The Modern Science of Mental Health"; “Scientology: A History of Man”

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Film: While watching someone run a pre-birth incident, Peggy tells Freddie that “we record everything” and indicates her pregnant belly. She continues, “through all lifetimes.”
Reality: In Dianetics (Book One) Hubbard talks at length about the “reactive mind” recording all experiences, even while in the womb. And the reactive mind records all past lives.

Reference: "Dianetics: The Modern Science of Mental Health"