The easy answer to your question is (maybe) yes and / or (maybe) no.
It all depends on what your warranty claim is in respect of. For instance, if you find that the instrument panel has failed, there is no direct link between it and the Power Commander, so all should be well.
If on the the other hand, the engine has burst, then KTM might (if they are so minded) reject your warranty claim on the grounds that your fitting of a Power Commander contributed to the failure.
Of course there is no certainty that KTM will, nor (if they do) are you under any obligation to accept their judgement on face value on day one. Consumer protection legislation is complex though, so you'll probably need some more technical advice should this unfortunate circumstance come to pass. Return to UKGSer (or visit a solicitor) if and when....
