While looking at the nuts and bolts of Trek to show the consistent irregularities of the machine's function is telling and true. It's not justification for a lack of reason in this situation. All that really says is "In for an inch, in for a mile."
So the question becomes..
If you really regard it as a wholesale failure of logic. Then why defend it when someone points out a large break in the logic if you know the machine itself is a rather clunky use of tools that could rather easily produce a working machine, why go against the truth?
I have to believe it's because you like the movie.
That really should stop playing a part in critique threads. If every thread is going to primarily center on a subject and that subject is always predicated on your like or dislike of the movie then every thread is ultimately the same...