It seems the risk would be if it wasn't the hard drive that failed but rather something on the motherboard, power regulation or something like that. If the warranty provider found Ubuntu or other O.S. on the hard drive and wanted to be difficult, could they take a position along these lines?
Originally Posted by craig10x
"We received your machine for warranty service. We found a failed power widget and replaced it. We then found an unapproved operating system installed. The unapproved operating system has not been tested on this machine and may permit/have caused power/thermal excursions beyond design limits of the power widget and caused its failure. Therefore warranty coverage is denied and the cost of the repair is $$$, payable now."
I don't know how likely the above scenario is but I've had experience with warranty providers being 'creative' in their denial of warranty repair. One way around this risk is to install a different hard drive in the new machine and install the non-standard O.S. on that. Then if there's a hardware issue, re-install the original hard drive before returning for warranty service. That may not be an inexpensive option though.