Guidelines are guidelines.
If you follow the guidelines, you are leveraging the platform's consistency. This reduces the cognitive load for your users because they already have an innate understanding of how to use your app, and because your app is more likely to feel like it fits along with everything else on their phone.
If you choose not to follow the guidelines, be able to clearly articulate why you're not following them. "I don't want to" is probably not a good reason. Keep your user's experience first and foremost in your mind. After all, the guidelines are for general app development, and they don't necessarily make sense for every application or every workflow. Any app should be user tested; this is more important the further that you get from the guidelines. If users aren't able to find an important control because you've chosen not to use the system controls, you might need to re-think some aspects of your design. If you have a well-articulated case for why the guidelines don't fit, and if you have data from user tests to back up breaking the guidelines, your boss and clients are going to be a lot more comfortable.
There are many reasons for an app to get rejected by the App Store. They're often easy to fix. Don't treat a rejection from the App Store like it's the end of the world. Accept that it's a possibility, and be responsive to it if it does happen. Don't waste your time worrying about it happening. Spend your time on creating and testing an awesome user experience.