Here's the thing. If you use one of those elements on a ship in your story it is perfectly fine. If you use all of those elements on your ship then you have an obvious connection to Star Trek. If I wrote a space opera in which a monk of a religious sect weilded a light sword composed of his channeled inner energy and battled a cyborg, it would be impossible to miss the Star Wars similarities, regardless of how different the actual specifics were.
On the other hand, Terry Brooks is constantly accused of ripping off LOTR, but his books are great.
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