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Highly unlikely that HFC's could do anything to negatively affect the motor. They are, however, illegal in most states as you're messing around with the emissions of the car. HFC's do make the car manufacturer's case a lot easier though in the event that they want to deny warranty coverage.
A tune and pulley have much more direct effects on the car, and I would never trust a salesman's word on those not voiding warranty. Frankly, I'm surprised he/she would say that. A tune would make it very easy for BMW to deny warranty coverage if they wanted to. Not so much a pulley, but if your power steering goes bad, forget about it.
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