The “flying spaghetti monster” was making a slightly different point.
Scientology was created to prove how gullible people are.
FSM was created as a example of how, in scientific discussions, if you accept ANY religion you have to accept ALL religions, no matter how silly. Science, by definition is the definition of the rules of the physical universe. Religion, by definition, is the definition of the rules of the spiritual universe as it spills over to the physical universe.
The FSM was a somewhat humorous example created to make that point.