It really depends on how much your rejection leads to a better user experience.
HIG will help you create an application that users will understand how to use more or less from the very beginning, and make the application easy to use.
If you do some things that improve life for the user, Apple will probably let him go. But if you deviate in such a way that the application is harder to use, they tend to decline on you.
Many possible deviations are fairly reasonable things - for example, I was rejected once for a rotated view, where the user interface elements did not completely replace everything correctly. After the fix (and it really was a mistake on my part), the application was accepted.
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