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On a membrane roof still under warranty, the mounting decision is made by the roofer, not the solar contractor. Here is how we run it.

Most commercial roofs we work on are TPO or PVC membrane with years left on the warranty. That single fact decides how the array is held down.
Penetrating a warranted membrane means bringing the roofer in to flash every stanchion and, on most warranties, re-certifying the roof afterwards. Ballast avoids both, at the cost of a structural review.
When penetration is unavoidable we bring the roofing manufacturer into the design review before drawings are stamped, and the flashing is done by their approved contractor. It costs more and it keeps the warranty intact.
On a warranted membrane the mounting decision belongs to the roofer. We design around their answer.