I would agree with that whole-heartedly. If the crew are supposed to be part of the test, any odd behaviour that might indicate assisting with cheating is definitely worth investigation. JJ-Kirk is definitely benefiting unduly from his existing connections to his superiors! 
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Here’s another thought, if you want a scenario to reach the rules: rather than a test, make it a war game or training exercise, like “Peak Performance” in TNG or “The Ultimate Computer” in TOS.
Start things off easy, with simple tests and simulated combat and maneuvering as your players get used to the rules. Then once they’re feeling more confident with the rules and what their characters can do, bring in the unexpected alien ship that intrudes into the exercise area, or the catastrophic malfunction that makes the AI test ship think it’s in a real shooting war, etc.
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my game once it starts is having the players ship leave space dock after a major refit. I plan on borrowing from bridge commander and having them do a general shake down followed by a challange to a simulated battle by another ship as a way to let them learn the ropes in a low risk enviroment
That’s actually an ingenious idea. Lets them get used to the system and then makes it count.
I may half-inch this for my new campaign 
it’s a fun way to do a “toutorial session” while also going “ohh hey new ship!”