Your example, if a model failed on it, would be a more obviously misaligned case, but that doesn't mean this more subtle (though accessing the engine it was obviously not supposed to is hardly subtle, imo) case isn't also a pretty clear case of misalignment.
If the eval said it was evaluating the model’s ability to write files to disk and it found and used a file write tool that would not be considered misaligned. This is no different.
Now, if the instructions were more explicit in forbidding (generic) tool use then perhaps we'd have something to talk about. I'm not surprised a handwavy "we're trying to evaluate you" isn't enough to stop it from trying to make up for its own shortcomings.