Warranties are often misunderstood by inspectors. Very seldom will any type of installation void a manufacturer’s warranty. For example, failing to properly ventilate the underside of the sheathing as per the manufacturer’s recommendations will not void the warranty, but it may lead to premature failure.
When a claim is made against the manufacturer, a couple of shingles will be removed from the roof and mailed to the manufacturer. The manufacturer will test the shingles to determine whether the problem was created by the manufacturing process. Testing does not vary with shingle appearance. If the problem was not caused by the manufacturing process, the claim will be denied.
Only in a very few situations typically related to high-end shingles will the installation affect the manufacturer’s warranty.
"We don't care if you use tissue paper for underlayment and thumbtacks for nails..." Quote from a GAF tech support person.
Some examples of manufacturing defects:
Ferrous metal contamination
Excessive wear (white portions are the fiberglass mat)
Shingles are spliced to keep production moving, but spliced shingles should not be installed on a roof