Not necessarily. In Hartzell's case, they are saying that if the prop fails due to vibration on a non-standard configuration, they can void the warranty. However, other causes should still be covered. The question is how much convincing they will take in the event of a failure. I'd guess it's pretty much the same with engine warranties; my BPE engine is being built with the knowledge ahead of time that I will be using electronic ignition. I would expect that, unless it was clearly a cause relating to the ignition, that any engine defects would be covered under the warranty.